diff --git a/.gitignore b/.gitignore
index eb9e98910e679749a1ae2334df8842db3379cc83..0e4fcedb3db933903779a4b43320218eb091df19 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,7 +7,8 @@ git.properties
# Vim
*.swp
# IntelliJ
-.idea/workspace.xml
+.idea/*
+*.iml
/target/
/public/target/
/protected/target/
diff --git a/.idea/compiler.xml b/.idea/compiler.xml
deleted file mode 100644
index dfc5c1cfab117046737e11860d9453db644e7354..0000000000000000000000000000000000000000
--- a/.idea/compiler.xml
+++ /dev/null
@@ -1,41 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="CompilerConfiguration">
- <option name="DEFAULT_COMPILER" value="Javac" />
- <resourceExtensions />
- <wildcardResourcePatterns>
- <entry name="!?*.java" />
- <entry name="!?*.form" />
- <entry name="!?*.class" />
- <entry name="!?*.groovy" />
- <entry name="!?*.scala" />
- <entry name="!?*.flex" />
- <entry name="!?*.kt" />
- <entry name="!?*.clj" />
- </wildcardResourcePatterns>
- <annotationProcessing>
- <profile default="true" name="Default" enabled="false">
- <processorPath useClasspath="true" />
- </profile>
- <profile default="false" name="Maven default annotation processors profile" enabled="false">
- <sourceOutputDir name="target/generated-sources/annotations" />
- <sourceTestOutputDir name="target/generated-test-sources/test-annotations" />
- <outputRelativeToContentRoot value="true" />
- <processorPath useClasspath="true" />
- <module name="BamMetrics" />
- <module name="Basty" />
- <module name="BiopetFramework" />
- <module name="BiopetGatkExtensions" />
- <module name="BiopetGatkPipelines" />
- <module name="BiopetProtectedPackage" />
- <module name="BiopetPublicPackage" />
- <module name="Flexiprep" />
- <module name="Gentrap" />
- <module name="Mapping" />
- <module name="Sage" />
- <module name="Yamsvp" />
- </profile>
- </annotationProcessing>
- </component>
-</project>
-
diff --git a/.idea/copyright/profiles_settings.xml b/.idea/copyright/profiles_settings.xml
deleted file mode 100644
index e7bedf3377d40335424fd605124d4761390218bb..0000000000000000000000000000000000000000
--- a/.idea/copyright/profiles_settings.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<component name="CopyrightManager">
- <settings default="" />
-</component>
\ No newline at end of file
diff --git a/.idea/encodings.xml b/.idea/encodings.xml
deleted file mode 100644
index 011e774a84ca0d7a1c7b3affd36a1f1d95a35da2..0000000000000000000000000000000000000000
--- a/.idea/encodings.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="Encoding" useUTFGuessing="true" native2AsciiForPropertiesFiles="false">
- <file url="file://$PROJECT_DIR$" charset="UTF-8" />
- <file url="file://$PROJECT_DIR$/protected" charset="UTF-8" />
- <file url="file://$PROJECT_DIR$/protected/basty" charset="UTF-8" />
- <file url="file://$PROJECT_DIR$/protected/biopet-gatk-extensions" charset="UTF-8" />
- <file url="file://$PROJECT_DIR$/protected/biopet-gatk-pipelines" charset="UTF-8" />
- <file url="file://$PROJECT_DIR$/protected/biopet-protected-package" charset="UTF-8" />
- <file url="file://$PROJECT_DIR$/public" charset="UTF-8" />
- <file url="file://$PROJECT_DIR$/public/bammetrics" charset="UTF-8" />
- <file url="file://$PROJECT_DIR$/public/biopet-framework" charset="UTF-8" />
- <file url="file://$PROJECT_DIR$/public/biopet-public-package" charset="UTF-8" />
- <file url="file://$PROJECT_DIR$/public/flexiprep" charset="UTF-8" />
- <file url="file://$PROJECT_DIR$/public/gentrap" charset="UTF-8" />
- <file url="file://$PROJECT_DIR$/public/mapping" charset="UTF-8" />
- <file url="file://$PROJECT_DIR$/public/sage" charset="UTF-8" />
- <file url="file://$PROJECT_DIR$/public/yamsvp" charset="UTF-8" />
- </component>
-</project>
-
diff --git a/.idea/libraries/Maven__colt_colt_1_2_0.xml b/.idea/libraries/Maven__colt_colt_1_2_0.xml
deleted file mode 100644
index 58562acd7c86c51f421cb507b2009b352e053d5a..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__colt_colt_1_2_0.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: colt:colt:1.2.0">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/colt/colt/1.2.0/colt-1.2.0.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/colt/colt/1.2.0/colt-1.2.0-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/colt/colt/1.2.0/colt-1.2.0-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__com_beust_jcommander_1_27.xml b/.idea/libraries/Maven__com_beust_jcommander_1_27.xml
deleted file mode 100644
index f0f9060d98726f4254ecec1e77e5b203501c82c9..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__com_beust_jcommander_1_27.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: com.beust:jcommander:1.27">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/com/beust/jcommander/1.27/jcommander-1.27.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/com/beust/jcommander/1.27/jcommander-1.27-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/com/beust/jcommander/1.27/jcommander-1.27-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__com_github_julien_truffaut_monocle_core_2_11_0_5_0.xml b/.idea/libraries/Maven__com_github_julien_truffaut_monocle_core_2_11_0_5_0.xml
deleted file mode 100644
index 4a6e5b1ee05fa235f4568b2e88f39d10a6d77a53..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__com_github_julien_truffaut_monocle_core_2_11_0_5_0.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/com/github/julien-truffaut/monocle-core_2.11/0.5.0/monocle-core_2.11-0.5.0.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/com/github/julien-truffaut/monocle-core_2.11/0.5.0/monocle-core_2.11-0.5.0-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/com/github/julien-truffaut/monocle-core_2.11/0.5.0/monocle-core_2.11-0.5.0-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__com_github_scopt_scopt_2_10_3_2_0.xml b/.idea/libraries/Maven__com_github_scopt_scopt_2_10_3_2_0.xml
deleted file mode 100644
index adf0f2cb7b4815a14a861c861b17af0d0985ad94..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__com_github_scopt_scopt_2_10_3_2_0.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: com.github.scopt:scopt_2.10:3.2.0">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/com/github/scopt/scopt_2.10/3.2.0/scopt_2.10-3.2.0.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/com/github/scopt/scopt_2.10/3.2.0/scopt_2.10-3.2.0-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/com/github/scopt/scopt_2.10/3.2.0/scopt_2.10-3.2.0-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__com_google_code_cofoja_cofoja_1_0_r139.xml b/.idea/libraries/Maven__com_google_code_cofoja_cofoja_1_0_r139.xml
deleted file mode 100644
index b7084f04b788d8bfa2618f851bce6582956043d9..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__com_google_code_cofoja_cofoja_1_0_r139.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: com.google.code.cofoja:cofoja:1.0-r139">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__com_google_code_gson_gson_2_2_2.xml b/.idea/libraries/Maven__com_google_code_gson_gson_2_2_2.xml
deleted file mode 100644
index b6113ec4a0af529eaa62b72c5aad18d774e66b60..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__com_google_code_gson_gson_2_2_2.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: com.google.code.gson:gson:2.2.2">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/com/google/code/gson/gson/2.2.2/gson-2.2.2.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/com/google/code/gson/gson/2.2.2/gson-2.2.2-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/com/google/code/gson/gson/2.2.2/gson-2.2.2-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__com_google_guava_guava_18_0.xml b/.idea/libraries/Maven__com_google_guava_guava_18_0.xml
deleted file mode 100644
index bbd71d77e995b85a163660856a9d45a449599fcc..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__com_google_guava_guava_18_0.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: com.google.guava:guava:18.0">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/com/google/guava/guava/18.0/guava-18.0.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/com/google/guava/guava/18.0/guava-18.0-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/com/google/guava/guava/18.0/guava-18.0-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__com_jamesmurty_utils_java_xmlbuilder_0_4.xml b/.idea/libraries/Maven__com_jamesmurty_utils_java_xmlbuilder_0_4.xml
deleted file mode 100644
index a2a0c049077909bff2bc1d1407ad54add750c5b5..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__com_jamesmurty_utils_java_xmlbuilder_0_4.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/com/jamesmurty/utils/java-xmlbuilder/0.4/java-xmlbuilder-0.4.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/com/jamesmurty/utils/java-xmlbuilder/0.4/java-xmlbuilder-0.4-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/com/jamesmurty/utils/java-xmlbuilder/0.4/java-xmlbuilder-0.4-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__commons_codec_commons_codec_1_3.xml b/.idea/libraries/Maven__commons_codec_commons_codec_1_3.xml
deleted file mode 100644
index 36880019d0745fc81588ac4c15269fcc448c2f7c..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__commons_codec_commons_codec_1_3.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: commons-codec:commons-codec:1.3">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/commons-codec/commons-codec/1.3/commons-codec-1.3.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/commons-codec/commons-codec/1.3/commons-codec-1.3-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/commons-codec/commons-codec/1.3/commons-codec-1.3-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__commons_collections_commons_collections_3_2_1.xml b/.idea/libraries/Maven__commons_collections_commons_collections_3_2_1.xml
deleted file mode 100644
index 3caee7e547658dba7cc48a47d96dc95bd160a2cc..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__commons_collections_commons_collections_3_2_1.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: commons-collections:commons-collections:3.2.1">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/commons-collections/commons-collections/3.2.1/commons-collections-3.2.1.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/commons-collections/commons-collections/3.2.1/commons-collections-3.2.1-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/commons-collections/commons-collections/3.2.1/commons-collections-3.2.1-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__commons_httpclient_commons_httpclient_3_1.xml b/.idea/libraries/Maven__commons_httpclient_commons_httpclient_3_1.xml
deleted file mode 100644
index 66e653715c85dc6da7371688199b7a537885f202..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__commons_httpclient_commons_httpclient_3_1.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: commons-httpclient:commons-httpclient:3.1">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__commons_io_commons_io_2_1.xml b/.idea/libraries/Maven__commons_io_commons_io_2_1.xml
deleted file mode 100644
index 3b7814235f79df36e422ccda425a23414fcb28fb..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__commons_io_commons_io_2_1.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: commons-io:commons-io:2.1">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/commons-io/commons-io/2.1/commons-io-2.1.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/commons-io/commons-io/2.1/commons-io-2.1-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/commons-io/commons-io/2.1/commons-io-2.1-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__commons_lang_commons_lang_2_5.xml b/.idea/libraries/Maven__commons_lang_commons_lang_2_5.xml
deleted file mode 100644
index 055afe5d1c257b1d741b54d625dbc4bba60d45d9..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__commons_lang_commons_lang_2_5.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: commons-lang:commons-lang:2.5">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/commons-lang/commons-lang/2.5/commons-lang-2.5.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/commons-lang/commons-lang/2.5/commons-lang-2.5-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/commons-lang/commons-lang/2.5/commons-lang-2.5-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__commons_logging_commons_logging_1_1_1.xml b/.idea/libraries/Maven__commons_logging_commons_logging_1_1_1.xml
deleted file mode 100644
index b770f56aa973a210ba6b27bc867394d3695317ef..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__commons_logging_commons_logging_1_1_1.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: commons-logging:commons-logging:1.1.1">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__concurrent_concurrent_1_3_4.xml b/.idea/libraries/Maven__concurrent_concurrent_1_3_4.xml
deleted file mode 100644
index 4acbd2f600b44497f6b568992c5f9cb1fd322fde..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__concurrent_concurrent_1_3_4.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: concurrent:concurrent:1.3.4">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/concurrent/concurrent/1.3.4/concurrent-1.3.4.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/concurrent/concurrent/1.3.4/concurrent-1.3.4-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/concurrent/concurrent/1.3.4/concurrent-1.3.4-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__dom4j_dom4j_1_6_1.xml b/.idea/libraries/Maven__dom4j_dom4j_1_6_1.xml
deleted file mode 100644
index 14681ee84083f43045a16158c0e62720d8f4e0bd..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__dom4j_dom4j_1_6_1.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: dom4j:dom4j:1.6.1">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/dom4j/dom4j/1.6.1/dom4j-1.6.1.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/dom4j/dom4j/1.6.1/dom4j-1.6.1-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/dom4j/dom4j/1.6.1/dom4j-1.6.1-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__gov_nist_math_jama_1_0_2.xml b/.idea/libraries/Maven__gov_nist_math_jama_1_0_2.xml
deleted file mode 100644
index 1241df092cd5916b98f2abbe20ed4574d1b35694..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__gov_nist_math_jama_1_0_2.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: gov.nist.math:jama:1.0.2">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/gov/nist/math/jama/1.0.2/jama-1.0.2.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/gov/nist/math/jama/1.0.2/jama-1.0.2-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/gov/nist/math/jama/1.0.2/jama-1.0.2-sources.jar!/" />
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__io_argonaut_argonaut_2_11_6_1_M4.xml b/.idea/libraries/Maven__io_argonaut_argonaut_2_11_6_1_M4.xml
deleted file mode 100644
index fa8e4d1d2140be1bd2f4b8ce0e6459d6a6727b9a..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__io_argonaut_argonaut_2_11_6_1_M4.xml
+++ /dev/null
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__it_unimi_dsi_fastutil_6_5_3.xml b/.idea/libraries/Maven__it_unimi_dsi_fastutil_6_5_3.xml
deleted file mode 100644
index 8acac37bfde8a9d7741fc2537c62be6226a88276..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__it_unimi_dsi_fastutil_6_5_3.xml
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\ No newline at end of file
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deleted file mode 100644
index 180d5875610f253557ef6fcc09b830841b0a5373..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__javax_activation_activation_1_1.xml
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__javax_mail_mail_1_4_4.xml b/.idea/libraries/Maven__javax_mail_mail_1_4_4.xml
deleted file mode 100644
index 733c7110533c45c66f49d638259c6cd88a3bbc39..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__javax_mail_mail_1_4_4.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__junit_junit_4_10.xml b/.idea/libraries/Maven__junit_junit_4_10.xml
deleted file mode 100644
index ed8bf5fe7f8a4a5117ac81f4ce4364cb1ca7cef2..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__junit_junit_4_10.xml
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__log4j_log4j_1_2_15.xml b/.idea/libraries/Maven__log4j_log4j_1_2_15.xml
deleted file mode 100644
index c6024af8c412e351cc32fd3208c9541d8706b0d4..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__log4j_log4j_1_2_15.xml
+++ /dev/null
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__net_java_dev_jets3t_jets3t_0_8_1.xml b/.idea/libraries/Maven__net_java_dev_jets3t_jets3t_0_8_1.xml
deleted file mode 100644
index a8f5dbbf0ba964d3323e54a16a946ae7cbf79a95..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__net_java_dev_jets3t_jets3t_0_8_1.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__net_java_dev_jna_jna_3_2_7.xml b/.idea/libraries/Maven__net_java_dev_jna_jna_3_2_7.xml
deleted file mode 100644
index a1926c5478ef4ec9795372223d385693c103d644..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__net_java_dev_jna_jna_3_2_7.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__net_sf_jgrapht_jgrapht_0_8_3.xml b/.idea/libraries/Maven__net_sf_jgrapht_jgrapht_0_8_3.xml
deleted file mode 100644
index a8f63eb792325904f5f6b04da8e6e62252b1070b..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__net_sf_jgrapht_jgrapht_0_8_3.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_apache_ant_ant_1_8_2.xml b/.idea/libraries/Maven__org_apache_ant_ant_1_8_2.xml
deleted file mode 100644
index 5bdad0716175bcf73406ed028f87f75a725f4c85..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_apache_ant_ant_1_8_2.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_apache_commons_commons_email_1_2.xml b/.idea/libraries/Maven__org_apache_commons_commons_email_1_2.xml
deleted file mode 100644
index 9ae605beb8a480b500906f3e62037b85828a117c..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_apache_commons_commons_email_1_2.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_apache_commons_commons_jexl_2_1_1.xml b/.idea/libraries/Maven__org_apache_commons_commons_jexl_2_1_1.xml
deleted file mode 100644
index fbbed3d823b5c81cd613d637fe8acb21222465d4..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_apache_commons_commons_jexl_2_1_1.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_apache_commons_commons_math_2_2.xml b/.idea/libraries/Maven__org_apache_commons_commons_math_2_2.xml
deleted file mode 100644
index 8f3e3159f1ca74019c0330df89ece45fe308f323..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_apache_commons_commons_math_2_2.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_apache_httpcomponents_httpclient_4_1_1.xml b/.idea/libraries/Maven__org_apache_httpcomponents_httpclient_4_1_1.xml
deleted file mode 100644
index 60582aab3d7bf7eed3e98cf4f1c4022b612e1867..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_apache_httpcomponents_httpclient_4_1_1.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_apache_httpcomponents_httpcore_4_1.xml b/.idea/libraries/Maven__org_apache_httpcomponents_httpcore_4_1.xml
deleted file mode 100644
index 27f97fc563b547ff8482791b8fc0efeb20a966b3..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_apache_httpcomponents_httpcore_4_1.xml
+++ /dev/null
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_beanshell_bsh_2_0b4.xml b/.idea/libraries/Maven__org_beanshell_bsh_2_0b4.xml
deleted file mode 100644
index d6f17aa773644a328b19420d5e184213a85b4065..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_beanshell_bsh_2_0b4.xml
+++ /dev/null
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_biojava_biojava3_core_3_1_0.xml b/.idea/libraries/Maven__org_biojava_biojava3_core_3_1_0.xml
deleted file mode 100644
index 5e2f8eda6a5c5d58e8f0f94726d849c76f71c8f5..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_biojava_biojava3_core_3_1_0.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_biojava_biojava3_sequencing_3_1_0.xml b/.idea/libraries/Maven__org_biojava_biojava3_sequencing_3_1_0.xml
deleted file mode 100644
index dc48c1bc9783c2c1cd947de313827a1bc870f4d9..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_biojava_biojava3_sequencing_3_1_0.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_engine_3_3.xml b/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_engine_3_3.xml
deleted file mode 100644
index 71262e7df7e8dfe7522694bd43e90bcb5d5a33b5..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_engine_3_3.xml
+++ /dev/null
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_queue_3_3.xml b/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_queue_3_3.xml
deleted file mode 100644
index c7094ebb417e6df20d27fb41198296a5d622f7be..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_queue_3_3.xml
+++ /dev/null
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_queue_extensions_distribution_3_3.xml b/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_queue_extensions_distribution_3_3.xml
deleted file mode 100644
index 518c5089d1715f5f774fcdb6ceff1c3f9283e0e5..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_queue_extensions_distribution_3_3.xml
+++ /dev/null
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_queue_extensions_generator_3_3.xml b/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_queue_extensions_generator_3_3.xml
deleted file mode 100644
index 33cb50b235389ba77ccd3035726f5d2a4fc442da..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_queue_extensions_generator_3_3.xml
+++ /dev/null
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_tools_protected_3_3.xml b/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_tools_protected_3_3.xml
deleted file mode 100644
index 5c18cfbe548d01ecab7173a7ab5378766c15850b..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_tools_protected_3_3.xml
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@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_tools_public_3_3.xml b/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_tools_public_3_3.xml
deleted file mode 100644
index cf56f34032742e45c039c07715af206639727a5d..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_tools_public_3_3.xml
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_utils_3_3.xml b/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_utils_3_3.xml
deleted file mode 100644
index 2bc8369715490e17188a67403e9b5d650a3eb5ee..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_broadinstitute_gatk_gatk_utils_3_3.xml
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_freemarker_freemarker_2_3_18.xml b/.idea/libraries/Maven__org_freemarker_freemarker_2_3_18.xml
deleted file mode 100644
index 2a73a605bcc98c75de52ad366859faa2a6950bee..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_freemarker_freemarker_2_3_18.xml
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_hamcrest_hamcrest_core_1_1.xml b/.idea/libraries/Maven__org_hamcrest_hamcrest_core_1_1.xml
deleted file mode 100644
index acdf44300b42ccd0a7dec6d5b31ed08c48e2b071..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_hamcrest_hamcrest_core_1_1.xml
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_javassist_javassist_3_16_1_GA.xml b/.idea/libraries/Maven__org_javassist_javassist_3_16_1_GA.xml
deleted file mode 100644
index 7b4e548b9893c05fae522fb433f6be5f58d4344a..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_javassist_javassist_3_16_1_GA.xml
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_mockito_mockito_all_1_9_5.xml b/.idea/libraries/Maven__org_mockito_mockito_all_1_9_5.xml
deleted file mode 100644
index 7797878d7a6e42ddf7b4bca81d9b434485b1c1f9..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_mockito_mockito_all_1_9_5.xml
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_reflections_reflections_0_9_9_RC1.xml b/.idea/libraries/Maven__org_reflections_reflections_0_9_9_RC1.xml
deleted file mode 100644
index 95dd64abf617040b0f2954440277da6d0d2acf92..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_reflections_reflections_0_9_9_RC1.xml
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_scala_lang_modules_scala_parser_combinators_2_11_1_0_2.xml b/.idea/libraries/Maven__org_scala_lang_modules_scala_parser_combinators_2_11_1_0_2.xml
deleted file mode 100644
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--- a/.idea/libraries/Maven__org_scala_lang_modules_scala_parser_combinators_2_11_1_0_2.xml
+++ /dev/null
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_scala_lang_modules_scala_xml_2_11_1_0_2.xml b/.idea/libraries/Maven__org_scala_lang_modules_scala_xml_2_11_1_0_2.xml
deleted file mode 100644
index 1a53cbb1de6052595e4ea5b0b0b3cf9908ce26e4..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_scala_lang_modules_scala_xml_2_11_1_0_2.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_scala_lang_scala_compiler_2_10_2.xml b/.idea/libraries/Maven__org_scala_lang_scala_compiler_2_10_2.xml
deleted file mode 100644
index f5312b6e0e989c218ade69f88e6a3c27fb89e363..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_scala_lang_scala_compiler_2_10_2.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_scala_lang_scala_library_2_11_2.xml b/.idea/libraries/Maven__org_scala_lang_scala_library_2_11_2.xml
deleted file mode 100644
index c2e5403fca7594c3ebd3a04af4eb51aacde2b881..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_scala_lang_scala_library_2_11_2.xml
+++ /dev/null
@@ -1,20 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_scala_lang_scala_reflect_2_10_2.xml b/.idea/libraries/Maven__org_scala_lang_scala_reflect_2_10_2.xml
deleted file mode 100644
index fc0e78ded0f8e14d51c25321a487b738f18c273f..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_scala_lang_scala_reflect_2_10_2.xml
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_scala_lang_scala_reflect_2_11_2.xml b/.idea/libraries/Maven__org_scala_lang_scala_reflect_2_11_2.xml
deleted file mode 100644
index ef190f1c4ffc8318d5d8164fc85b3457dfe3653a..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_scala_lang_scala_reflect_2_11_2.xml
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_scalatest_scalatest_2_11_2_2_1.xml b/.idea/libraries/Maven__org_scalatest_scalatest_2_11_2_2_1.xml
deleted file mode 100644
index 5f9b531f3518dd36dc37f1074e140c4a8121b7e1..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_scalatest_scalatest_2_11_2_2_1.xml
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_scalaz_scalaz_core_2_11_7_1_0.xml b/.idea/libraries/Maven__org_scalaz_scalaz_core_2_11_7_1_0.xml
deleted file mode 100644
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--- a/.idea/libraries/Maven__org_scalaz_scalaz_core_2_11_7_1_0.xml
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_simpleframework_simple_xml_2_0_4.xml b/.idea/libraries/Maven__org_simpleframework_simple_xml_2_0_4.xml
deleted file mode 100644
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--- a/.idea/libraries/Maven__org_simpleframework_simple_xml_2_0_4.xml
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_slf4j_slf4j_api_1_6_1.xml b/.idea/libraries/Maven__org_slf4j_slf4j_api_1_6_1.xml
deleted file mode 100644
index 38036e9fdaff30321ca95c8b83deb495d47921d0..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_slf4j_slf4j_api_1_6_1.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: org.slf4j:slf4j-api:1.6.1">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/org/slf4j/slf4j-api/1.6.1/slf4j-api-1.6.1.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/org/slf4j/slf4j-api/1.6.1/slf4j-api-1.6.1-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/org/slf4j/slf4j-api/1.6.1/slf4j-api-1.6.1-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_slf4j_slf4j_log4j12_1_6_1.xml b/.idea/libraries/Maven__org_slf4j_slf4j_log4j12_1_6_1.xml
deleted file mode 100644
index 2fbfdab3b61251c8fe45d3ce1edb593896c34f0c..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_slf4j_slf4j_log4j12_1_6_1.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: org.slf4j:slf4j-log4j12:1.6.1">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/org/slf4j/slf4j-log4j12/1.6.1/slf4j-log4j12-1.6.1.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/org/slf4j/slf4j-log4j12/1.6.1/slf4j-log4j12-1.6.1-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/org/slf4j/slf4j-log4j12/1.6.1/slf4j-log4j12-1.6.1-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_testng_testng_6_8.xml b/.idea/libraries/Maven__org_testng_testng_6_8.xml
deleted file mode 100644
index 7d6214c0cd6a81ba34622b59bb9c10851268d794..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_testng_testng_6_8.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: org.testng:testng:6.8">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/org/testng/testng/6.8/testng-6.8.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/org/testng/testng/6.8/testng-6.8-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/org/testng/testng/6.8/testng-6.8-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_xerial_snappy_snappy_java_1_0_3_rc3.xml b/.idea/libraries/Maven__org_xerial_snappy_snappy_java_1_0_3_rc3.xml
deleted file mode 100644
index dd59ad3bb36fe7086b6c51db973a58f831bdefa9..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_xerial_snappy_snappy_java_1_0_3_rc3.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/org/xerial/snappy/snappy-java/1.0.3-rc3/snappy-java-1.0.3-rc3.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/org/xerial/snappy/snappy-java/1.0.3-rc3/snappy-java-1.0.3-rc3-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/org/xerial/snappy/snappy-java/1.0.3-rc3/snappy-java-1.0.3-rc3-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_yaml_snakeyaml_1_6.xml b/.idea/libraries/Maven__org_yaml_snakeyaml_1_6.xml
deleted file mode 100644
index 0f8bd1980d563511f80d2e5cd3e903b81f9f1e70..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__org_yaml_snakeyaml_1_6.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: org.yaml:snakeyaml:1.6">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/org/yaml/snakeyaml/1.6/snakeyaml-1.6.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/org/yaml/snakeyaml/1.6/snakeyaml-1.6-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/org/yaml/snakeyaml/1.6/snakeyaml-1.6-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__picard_picard_1_120_1579.xml b/.idea/libraries/Maven__picard_picard_1_120_1579.xml
deleted file mode 100644
index 99e2c47c3166dab99d32cae1241985f6501e4f78..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__picard_picard_1_120_1579.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: picard:picard:1.120.1579">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/picard/picard/1.120.1579/picard-1.120.1579.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/picard/picard/1.120.1579/picard-1.120.1579-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/picard/picard/1.120.1579/picard-1.120.1579-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__samtools_htsjdk_1_120_1620.xml b/.idea/libraries/Maven__samtools_htsjdk_1_120_1620.xml
deleted file mode 100644
index 260b14fd5453aac02496f58254006016354d3fb1..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__samtools_htsjdk_1_120_1620.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: samtools:htsjdk:1.120.1620">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/samtools/htsjdk/1.120.1620/htsjdk-1.120.1620.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/samtools/htsjdk/1.120.1620/htsjdk-1.120.1620-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/samtools/htsjdk/1.120.1620/htsjdk-1.120.1620-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__stax_stax_1_2_0.xml b/.idea/libraries/Maven__stax_stax_1_2_0.xml
deleted file mode 100644
index ade036ec92b3baac0ff05b72a8f8c267a0af2a31..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__stax_stax_1_2_0.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: stax:stax:1.2.0">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/stax/stax/1.2.0/stax-1.2.0.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/stax/stax/1.2.0/stax-1.2.0-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/stax/stax/1.2.0/stax-1.2.0-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__stax_stax_api_1_0_1.xml b/.idea/libraries/Maven__stax_stax_api_1_0_1.xml
deleted file mode 100644
index 0b13335ee1567f514d4110b68a207cb48a3ae68b..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__stax_stax_api_1_0_1.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: stax:stax-api:1.0.1">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/stax/stax-api/1.0.1/stax-api-1.0.1.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/stax/stax-api/1.0.1/stax-api-1.0.1-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/stax/stax-api/1.0.1/stax-api-1.0.1-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__us_levk_drmaa_common_1_0.xml b/.idea/libraries/Maven__us_levk_drmaa_common_1_0.xml
deleted file mode 100644
index af511c454a532cbaccb35bb8a65d7d49286ca4c8..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__us_levk_drmaa_common_1_0.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: us.levk:drmaa-common:1.0">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/us/levk/drmaa-common/1.0/drmaa-common-1.0.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/us/levk/drmaa-common/1.0/drmaa-common-1.0-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/us/levk/drmaa-common/1.0/drmaa-common-1.0-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__us_levk_drmaa_gridengine_6_2u5.xml b/.idea/libraries/Maven__us_levk_drmaa_gridengine_6_2u5.xml
deleted file mode 100644
index a8f2903239f85ad95f27f061542fb9d6d8782c54..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__us_levk_drmaa_gridengine_6_2u5.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: us.levk:drmaa-gridengine:6.2u5">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/us/levk/drmaa-gridengine/6.2u5/drmaa-gridengine-6.2u5.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/us/levk/drmaa-gridengine/6.2u5/drmaa-gridengine-6.2u5-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/us/levk/drmaa-gridengine/6.2u5/drmaa-gridengine-6.2u5-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__xml_apis_xml_apis_1_0_b2.xml b/.idea/libraries/Maven__xml_apis_xml_apis_1_0_b2.xml
deleted file mode 100644
index c36e71714a7d641de87adc2d59533145c852f652..0000000000000000000000000000000000000000
--- a/.idea/libraries/Maven__xml_apis_xml_apis_1_0_b2.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
- <library name="Maven: xml-apis:xml-apis:1.0.b2">
- <CLASSES>
- <root url="jar://$MAVEN_REPOSITORY$/xml-apis/xml-apis/1.0.b2/xml-apis-1.0.b2.jar!/" />
- </CLASSES>
- <JAVADOC>
- <root url="jar://$MAVEN_REPOSITORY$/xml-apis/xml-apis/1.0.b2/xml-apis-1.0.b2-javadoc.jar!/" />
- </JAVADOC>
- <SOURCES>
- <root url="jar://$MAVEN_REPOSITORY$/xml-apis/xml-apis/1.0.b2/xml-apis-1.0.b2-sources.jar!/" />
- </SOURCES>
- </library>
-</component>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
deleted file mode 100644
index 8fb54ee42a504d86c34a2800c767c27a0b9318df..0000000000000000000000000000000000000000
--- a/.idea/misc.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="EntryPointsManager">
- <entry_points version="2.0" />
- </component>
- <component name="MavenProjectsManager">
- <option name="originalFiles">
- <list>
- <option value="$PROJECT_DIR$/pom.xml" />
- </list>
- </option>
- </component>
- <component name="ProjectRootManager" version="2" languageLevel="JDK_1_6" assert-keyword="true" jdk-15="true" project-jdk-name="1.7" project-jdk-type="JavaSDK" />
-</project>
-
diff --git a/.idea/modules.xml b/.idea/modules.xml
deleted file mode 100644
index c2791c238840930ce91491fe83bdcd299f953ce5..0000000000000000000000000000000000000000
--- a/.idea/modules.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="ProjectModuleManager">
- <modules>
- <module fileurl="file://$PROJECT_DIR$/public/bammetrics/BamMetrics.iml" filepath="$PROJECT_DIR$/public/bammetrics/BamMetrics.iml" />
- <module fileurl="file://$PROJECT_DIR$/protected/basty/Basty.iml" filepath="$PROJECT_DIR$/protected/basty/Basty.iml" />
- <module fileurl="file://$PROJECT_DIR$/public/Biopet.iml" filepath="$PROJECT_DIR$/public/Biopet.iml" />
- <module fileurl="file://$PROJECT_DIR$/public/biopet-framework/BiopetFramework.iml" filepath="$PROJECT_DIR$/public/biopet-framework/BiopetFramework.iml" />
- <module fileurl="file://$PROJECT_DIR$/protected/BiopetGatk.iml" filepath="$PROJECT_DIR$/protected/BiopetGatk.iml" />
- <module fileurl="file://$PROJECT_DIR$/protected/biopet-gatk-extensions/BiopetGatkExtensions.iml" filepath="$PROJECT_DIR$/protected/biopet-gatk-extensions/BiopetGatkExtensions.iml" />
- <module fileurl="file://$PROJECT_DIR$/protected/biopet-gatk-pipelines/BiopetGatkPipelines.iml" filepath="$PROJECT_DIR$/protected/biopet-gatk-pipelines/BiopetGatkPipelines.iml" />
- <module fileurl="file://$PROJECT_DIR$/protected/biopet-protected-package/BiopetProtectedPackage.iml" filepath="$PROJECT_DIR$/protected/biopet-protected-package/BiopetProtectedPackage.iml" />
- <module fileurl="file://$PROJECT_DIR$/public/biopet-public-package/BiopetPublicPackage.iml" filepath="$PROJECT_DIR$/public/biopet-public-package/BiopetPublicPackage.iml" />
- <module fileurl="file://$PROJECT_DIR$/BiopetRoot.iml" filepath="$PROJECT_DIR$/BiopetRoot.iml" />
- <module fileurl="file://$PROJECT_DIR$/public/flexiprep/Flexiprep.iml" filepath="$PROJECT_DIR$/public/flexiprep/Flexiprep.iml" />
- <module fileurl="file://$PROJECT_DIR$/public/gentrap/Gentrap.iml" filepath="$PROJECT_DIR$/public/gentrap/Gentrap.iml" />
- <module fileurl="file://$PROJECT_DIR$/public/mapping/Mapping.iml" filepath="$PROJECT_DIR$/public/mapping/Mapping.iml" />
- <module fileurl="file://$PROJECT_DIR$/public/sage/Sage.iml" filepath="$PROJECT_DIR$/public/sage/Sage.iml" />
- <module fileurl="file://$PROJECT_DIR$/public/yamsvp/Yamsvp.iml" filepath="$PROJECT_DIR$/public/yamsvp/Yamsvp.iml" />
- </modules>
- </component>
-</project>
-
diff --git a/.idea/scala_compiler.xml b/.idea/scala_compiler.xml
deleted file mode 100644
index b2cf5cfadc278c64be83b5a035dcf42fafd338b1..0000000000000000000000000000000000000000
--- a/.idea/scala_compiler.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="ScalaCompilerConfiguration">
- <option name="deprecationWarnings" value="true" />
- <option name="featureWarnings" value="true" />
- <parameters>
- <parameter value="-dependencyfile" />
- <parameter value="$MODULE_DIR$/target/.scala_dependencies" />
- <parameter value="-feature" />
- <parameter value="$PROJECT_DIR$/protected/biopet-gatk-extensions/target/.scala_dependencies" />
- <parameter value="$PROJECT_DIR$/protected/biopet-protected-package/target/.scala_dependencies" />
- <parameter value="$PROJECT_DIR$/protected/biopet-gatk-pipelines/target/.scala_dependencies" />
- <parameter value="$PROJECT_DIR$/protected/basty/target/.scala_dependencies" />
- </parameters>
- </component>
-</project>
\ No newline at end of file
diff --git a/.idea/scopes/scope_settings.xml b/.idea/scopes/scope_settings.xml
deleted file mode 100644
index 922003b8433bcad6ce9778a37628d738faa26389..0000000000000000000000000000000000000000
--- a/.idea/scopes/scope_settings.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<component name="DependencyValidationManager">
- <state>
- <option name="SKIP_IMPORT_STATEMENTS" value="false" />
- </state>
-</component>
\ No newline at end of file
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
deleted file mode 100644
index 9d32e507a9813290efcaf393d19f39eaa295ff9d..0000000000000000000000000000000000000000
--- a/.idea/vcs.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="VcsDirectoryMappings">
- <mapping directory="" vcs="" />
- <mapping directory="$PROJECT_DIR$" vcs="Git" />
- </component>
-</project>
-
diff --git a/BiopetRoot.iml b/BiopetRoot.iml
deleted file mode 100644
index 65b49ee12b35fb025f2ff7dee4698415bdc360e3..0000000000000000000000000000000000000000
--- a/BiopetRoot.iml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="false">
- <output url="file://$MODULE_DIR$/target/classes" />
- <output-test url="file://$MODULE_DIR$/target/test-classes" />
- <content url="file://$MODULE_DIR$">
- <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
- <excludeFolder url="file://$MODULE_DIR$/target" />
- </content>
- <orderEntry type="inheritedJdk" />
- <orderEntry type="sourceFolder" forTests="false" />
- </component>
-</module>
\ No newline at end of file
diff --git a/log4j.properties b/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/protected/BiopetGatk.iml b/protected/BiopetGatk.iml
deleted file mode 100644
index 65b49ee12b35fb025f2ff7dee4698415bdc360e3..0000000000000000000000000000000000000000
--- a/protected/BiopetGatk.iml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="false">
- <output url="file://$MODULE_DIR$/target/classes" />
- <output-test url="file://$MODULE_DIR$/target/test-classes" />
- <content url="file://$MODULE_DIR$">
- <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
- <excludeFolder url="file://$MODULE_DIR$/target" />
- </content>
- <orderEntry type="inheritedJdk" />
- <orderEntry type="sourceFolder" forTests="false" />
- </component>
-</module>
\ No newline at end of file
diff --git a/protected/basty/Basty.iml b/protected/basty/Basty.iml
deleted file mode 100644
index fb9121d5fa34a78471f7453cbf17fae04ab8a3e3..0000000000000000000000000000000000000000
--- a/protected/basty/Basty.iml
+++ /dev/null
@@ -1,97 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="false">
- <output url="file://$MODULE_DIR$/target/classes" />
- <output-test url="file://$MODULE_DIR$/target/test-classes" />
- <content url="file://$MODULE_DIR$">
- <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
- <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
- <excludeFolder url="file://$MODULE_DIR$/target" />
- </content>
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- <CLASSES>
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- </CLASSES>
- <JAVADOC />
- <SOURCES />
- </library>
- </orderEntry>
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" />
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- <orderEntry type="module" module-name="BiopetGatkPipelines" />
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- <orderEntry type="module" module-name="Mapping" />
- <orderEntry type="module" module-name="Flexiprep" />
- <orderEntry type="module" module-name="BamMetrics" />
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\ No newline at end of file
diff --git a/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala b/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
index 5088e44c2eca6f54b23104c7695c3a03d5f762c8..544af1b7c1e925f0bc21ccf7c75fa0669a32fe84 100644
--- a/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
+++ b/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
@@ -60,28 +60,34 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
}
def addMultiSampleJobs(): Unit = {
- val refVariants = addGenerateFasta(null, outputDir + "reference/", outputName = "reference")
- val refVariantSnps = addGenerateFasta(null, outputDir + "reference/", outputName = "reference", snpsOnly = true)
+ val refVariants = addGenerateFasta(null, new File(outputDir, "reference"), outputName = "reference")
+ val refVariantSnps = addGenerateFasta(null, new File(outputDir, "reference"), outputName = "reference", snpsOnly = true)
- val catVariants = Cat(this, refVariants.variants :: samples.map(_._2.output.variants).toList, outputDir + "fastas/variant.fasta")
+ val catVariants = Cat(this, refVariants.variants :: samples.map(_._2.output.variants).toList,
+ new File(outputDir, "fastas" + File.separator + "variant.fasta"))
add(catVariants)
- val catVariantsSnps = Cat(this, refVariantSnps.variants :: samples.map(_._2.outputSnps.variants).toList, outputDir + "fastas/variant.snps_only.fasta")
+ val catVariantsSnps = Cat(this, refVariantSnps.variants :: samples.map(_._2.outputSnps.variants).toList,
+ new File(outputDir, "fastas" + File.separator + "variant.snps_only.fasta"))
add(catVariantsSnps)
- val catConsensus = Cat(this, refVariants.consensus :: samples.map(_._2.output.consensus).toList, outputDir + "fastas/consensus.fasta")
+ val catConsensus = Cat(this, refVariants.consensus :: samples.map(_._2.output.consensus).toList,
+ new File(outputDir, "fastas" + File.separator + "consensus.fasta"))
add(catConsensus)
- val catConsensusSnps = Cat(this, refVariantSnps.consensus :: samples.map(_._2.outputSnps.consensus).toList, outputDir + "fastas/consensus.snps_only.fasta")
+ val catConsensusSnps = Cat(this, refVariantSnps.consensus :: samples.map(_._2.outputSnps.consensus).toList,
+ new File(outputDir, "fastas" + File.separator + "consensus.snps_only.fasta"))
add(catConsensusSnps)
- val catConsensusVariants = Cat(this, refVariants.consensusVariants :: samples.map(_._2.output.consensusVariants).toList, outputDir + "fastas/consensus.variant.fasta")
+ val catConsensusVariants = Cat(this, refVariants.consensusVariants :: samples.map(_._2.output.consensusVariants).toList,
+ new File(outputDir, "fastas" + File.separator + "consensus.variant.fasta"))
add(catConsensusVariants)
- val catConsensusVariantsSnps = Cat(this, refVariantSnps.consensusVariants :: samples.map(_._2.outputSnps.consensusVariants).toList, outputDir + "fastas/consensus.variant.snps_only.fasta")
+ val catConsensusVariantsSnps = Cat(this, refVariantSnps.consensusVariants :: samples.map(_._2.outputSnps.consensusVariants).toList,
+ new File(outputDir, "fastas" + File.separator + "consensus.variant.snps_only.fasta"))
add(catConsensusVariantsSnps)
val seed: Int = config("seed", default = 12345)
- def addTreeJobs(variants: File, concensusVariants: File, outputDir: String, outputName: String) {
- val dirSufixRaxml = if (outputDir.endsWith(File.separator)) "raxml" else File.separator + "raxml"
- val dirSufixGubbins = if (outputDir.endsWith(File.separator)) "gubbins" else File.separator + "gubbins"
+ def addTreeJobs(variants: File, concensusVariants: File, outputDir: File, outputName: String) {
+ val dirSufixRaxml = new File(outputDir, "raxml")
+ val dirSufixGubbins = new File(outputDir, "gubbins")
val raxmlMl = new Raxml(this)
raxmlMl.input = variants
@@ -101,7 +107,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
raxmlBoot.m = config("raxml_ml_model", default = "GTRGAMMAX")
raxmlBoot.p = seed
raxmlBoot.b = math.abs(r.nextInt)
- raxmlBoot.w = outputDir + dirSufixRaxml
+ raxmlBoot.w = dirSufixRaxml
raxmlBoot.N = 1
raxmlBoot.n = outputName + "_boot_" + t
add(raxmlBoot)
@@ -125,16 +131,18 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
val gubbins = new RunGubbins(this)
gubbins.fastafile = concensusVariants
gubbins.startingTree = Some(raxmlBi.getBipartitionsFile)
- gubbins.outputDirectory = outputDir + dirSufixGubbins
+ gubbins.outputDirectory = dirSufixGubbins
add(gubbins)
}
- addTreeJobs(catVariantsSnps.output, catConsensusVariantsSnps.output, outputDir + "trees" + File.separator + "snps_only", "snps_only")
- addTreeJobs(catVariants.output, catConsensusVariants.output, outputDir + "trees" + File.separator + "snps_indels", "snps_indels")
+ addTreeJobs(catVariantsSnps.output, catConsensusVariantsSnps.output,
+ new File(outputDir, "trees" + File.separator + "snps_only"), "snps_only")
+ addTreeJobs(catVariants.output, catConsensusVariants.output,
+ new File(outputDir, "trees" + File.separator + "snps_indels"), "snps_indels")
}
- def addGenerateFasta(sampleName: String, outputDir: String, outputName: String = null,
+ def addGenerateFasta(sampleName: String, outputDir: File, outputName: String = null,
snpsOnly: Boolean = false): FastaOutput = {
val bastyGenerateFasta = new BastyGenerateFasta(this)
bastyGenerateFasta.outputName = if (outputName != null) outputName else sampleName
diff --git a/protected/basty/src/test/resources/log4j.properties b/protected/basty/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/protected/basty/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/protected/biopet-gatk-extensions/BiopetGatkExtensions.iml b/protected/biopet-gatk-extensions/BiopetGatkExtensions.iml
deleted file mode 100644
index 93f504d0422488b4a3c8dba634ced25e639c678b..0000000000000000000000000000000000000000
--- a/protected/biopet-gatk-extensions/BiopetGatkExtensions.iml
+++ /dev/null
@@ -1,92 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="false">
- <output url="file://$MODULE_DIR$/target/classes" />
- <output-test url="file://$MODULE_DIR$/target/test-classes" />
- <content url="file://$MODULE_DIR$">
- <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
- <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
- <excludeFolder url="file://$MODULE_DIR$/target" />
- </content>
- <orderEntry type="inheritedJdk" />
- <orderEntry type="sourceFolder" forTests="false" />
- <orderEntry type="module" module-name="BiopetFramework" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" />
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- <CLASSES>
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- <JAVADOC />
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- <SOURCES />
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- </orderEntry>
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\ No newline at end of file
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala
index 8728b6c651824e340556222cb60ef52d7fd9ab0a..ccdce3411d3df623657b3cd2a14415cf67f7b134 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala
@@ -11,8 +11,8 @@ import nl.lumc.sasc.biopet.core.config.Configurable
class ApplyRecalibration(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.ApplyRecalibration with GatkGeneral {
scatterCount = config("scattercount", default = 0)
- override def afterGraph {
- super.afterGraph
+ override def beforeGraph {
+ super.beforeGraph
nt = Option(getThreads(3))
memoryLimit = Option(nt.getOrElse(1) * 2)
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
index c07a2a66c363fe9623ad35225e9f76eb45aa67a4..e6cc3aaf64790aea8198f60d57d75df4c47082f1 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
@@ -22,7 +22,7 @@ object BaseRecalibrator {
val br = new BaseRecalibrator(root)
br.input_file :+= input
br.out = output
- br.afterGraph
+ br.beforeGraph
return br
}
}
\ No newline at end of file
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
index 147398ac798c077da0722b2078f7ea21c666b7d1..3d1b5585028f69c01934f0ddfc0d54c6a9c25169 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
@@ -13,13 +13,13 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
override def subPath = "gatk" :: super.subPath
- jarFile = config("gatk_jar", required = true)
+ jarFile = config("gatk_jar")
override val defaultVmem = "7G"
if (config.contains("intervals")) intervals = config("intervals").asFileList
if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
- reference_sequence = config("reference", required = true)
+ reference_sequence = config("reference")
if (config.contains("gatk_key")) gatk_key = config("gatk_key")
if (config.contains("pedigree")) pedigree = config("pedigree").asFileList
}
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
index b8f4ea4efa3ea8cfed563c2b82651c0001b794f7..9521e9ea0f0d09b49690a9f6ea977f13a6eb3b8d 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
@@ -35,13 +35,13 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
stand_emit_conf = config("stand_emit_conf", default = 0)
}
- override def afterGraph {
- super.afterGraph
+ override def beforeGraph {
+ super.beforeGraph
if (bamOutput != null && nct.getOrElse(1) > 1) {
threads = 1
logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
}
- nct = Some(threads)
+ nct = Some(getThreads(1))
memoryLimit = Option(memoryLimit.getOrElse(2.0) * nct.getOrElse(1))
}
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala
index fb5eb4cc89a716bc30e4c90d4578326ed0b71d42..315934f8d4d09178c3200e1e1f904a7a865e59bb 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala
@@ -13,7 +13,7 @@ class IndelRealigner(val root: Configurable) extends org.broadinstitute.gatk.que
}
object IndelRealigner {
- def apply(root: Configurable, input: File, targetIntervals: File, outputDir: String): IndelRealigner = {
+ def apply(root: Configurable, input: File, targetIntervals: File, outputDir: File): IndelRealigner = {
val ir = new IndelRealigner(root)
ir.input_file :+= input
ir.targetIntervals = targetIntervals
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/RealignerTargetCreator.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/RealignerTargetCreator.scala
index bfd53fd6ee6761c3b7697c5277bef0a9af244784..76998f41d0c696df6bc06dfb8ff322331bd2ad47 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/RealignerTargetCreator.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/RealignerTargetCreator.scala
@@ -18,7 +18,7 @@ class RealignerTargetCreator(val root: Configurable) extends org.broadinstitute.
}
object RealignerTargetCreator {
- def apply(root: Configurable, input: File, outputDir: String): RealignerTargetCreator = {
+ def apply(root: Configurable, input: File, outputDir: File): RealignerTargetCreator = {
val re = new RealignerTargetCreator(root)
re.input_file :+= input
re.out = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.intervals")
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
index 26936df755a3d25aa41f78e0c2b568920b93e585..599ffa170519c17d7b3e35e14783ad75e208dadb 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
@@ -8,14 +8,14 @@ package nl.lumc.sasc.biopet.extensions.gatk
import nl.lumc.sasc.biopet.core.config.Configurable
class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.UnifiedGenotyper with GatkGeneral {
- override def afterGraph {
- super.afterGraph
+ override def beforeGraph {
+ super.beforeGraph
genotype_likelihoods_model = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.BOTH
if (config.contains("scattercount")) scatterCount = config("scattercount")
if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
this.sample_ploidy = config("ploidy")
- nct = config("threads", default = 1)
+ nct = Some(getThreads(1))
memoryLimit = Option(nct.getOrElse(1) * 2)
if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
if (config.contains("output_mode")) {
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
index c7956cab19dde275c322f3196eafe4ddce60800f..a9d252fde235f347c16ac3ea1d6b7e346c3214ff 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
@@ -9,8 +9,8 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {
- override def afterGraph {
- super.afterGraph
+ override def beforeGraph {
+ super.beforeGraph
}
}
@@ -21,7 +21,7 @@ object VariantEval {
vareval.eval = Seq(sample)
vareval.comp = Seq(compareWith)
vareval.out = output
- vareval.afterGraph
+ vareval.beforeGraph
return vareval
}
@@ -35,7 +35,7 @@ object VariantEval {
vareval.ST = ST
vareval.noEV = true
vareval.EV = EV
- vareval.afterGraph
+ vareval.beforeGraph
return vareval
}
diff --git a/protected/biopet-gatk-extensions/src/test/resources/log4j.properties b/protected/biopet-gatk-extensions/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/protected/biopet-gatk-extensions/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/protected/biopet-gatk-pipelines/BiopetGatkPipelines.iml b/protected/biopet-gatk-pipelines/BiopetGatkPipelines.iml
deleted file mode 100644
index 326e841ffaa063db06bb7de76a633504ef5f79f2..0000000000000000000000000000000000000000
--- a/protected/biopet-gatk-pipelines/BiopetGatkPipelines.iml
+++ /dev/null
@@ -1,96 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="false">
- <output url="file://$MODULE_DIR$/target/classes" />
- <output-test url="file://$MODULE_DIR$/target/test-classes" />
- <content url="file://$MODULE_DIR$">
- <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
- <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
- <excludeFolder url="file://$MODULE_DIR$/target" />
- </content>
- <orderEntry type="inheritedJdk" />
- <orderEntry type="sourceFolder" forTests="false" />
- <orderEntry type="module" module-name="BiopetFramework" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" />
- <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" />
- <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" />
- <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" />
- <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" />
- <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" />
- <orderEntry type="module-library">
- <library name="Maven: com.sun:tools:1.4.2">
- <CLASSES>
- <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" />
- </CLASSES>
- <JAVADOC />
- <SOURCES />
- </library>
- </orderEntry>
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" />
- <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" />
- <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" />
- <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" />
- <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" />
- <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" />
- <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" />
- <orderEntry type="module-library">
- <library name="Maven: com.sun:tools.jar:1.5">
- <CLASSES>
- <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" />
- </CLASSES>
- <JAVADOC />
- <SOURCES />
- </library>
- </orderEntry>
- <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" />
- <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" />
- <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" />
- <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" />
- <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" />
- <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" />
- <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
- <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" />
- <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
- <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" />
- <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" />
- <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" />
- <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" />
- <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" />
- <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" />
- <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" />
- <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" />
- <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
- <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" />
- <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" />
- <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" />
- <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" />
- <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" />
- <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" />
- <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" />
- <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" />
- <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" />
- <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" />
- <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" />
- <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" />
- <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" />
- <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" />
- <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" />
- <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" />
- <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" />
- <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
- <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" />
- <orderEntry type="module" module-name="BiopetGatkExtensions" />
- <orderEntry type="module" module-name="Mapping" />
- <orderEntry type="module" module-name="Flexiprep" />
- <orderEntry type="module" module-name="BamMetrics" />
- </component>
-</module>
\ No newline at end of file
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
index a054a8703778b8d71a9a778a56960b798f9c9e5e..342dabcdad82ebb78e28a41c360ef13a3568069d 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
@@ -29,11 +29,8 @@ class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with Biope
var dbsnp: File = config("dbsnp")
def init() {
- if (config.contains("gvcffiles")) for (file <- config("gvcffiles").asList) {
+ if (config.contains("gvcffiles")) for (file <- config("gvcffiles").asList)
gvcfFiles ::= file.toString
- }
- if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
- else if (!outputDir.endsWith("/")) outputDir += "/"
}
def biopetScript() {
@@ -53,7 +50,7 @@ class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with Biope
val gatkGenotyping = new GatkGenotyping(this)
gatkGenotyping.inputGvcfs = sampleGvcf :: gvcfPool
gatkGenotyping.samples :+= sampleName
- gatkGenotyping.outputDir = outputDir + "samples_" + gvcfPool.size + "/"
+ gatkGenotyping.outputDir = new File(outputDir, "samples_" + gvcfPool.size)
gatkGenotyping.init
gatkGenotyping.biopetScript
addAll(gatkGenotyping.functions)
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
index 0143d1bb63417956ec2a6d3d079a17b0b2f63d5e..7fcebd54afb8e18b3cf5236e4210001c9882b689 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
@@ -33,16 +33,15 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
var samples: List[String] = Nil
def init() {
- if (outputFile == null) outputFile = outputDir + outputName + ".vcf.gz"
- if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
- else if (!outputDir.endsWith("/")) outputDir += "/"
+ require(outputName != null, "Outputname is null")
+ if (outputFile == null) outputFile = new File(outputDir, outputName + ".vcf.gz")
}
def biopetScript() {
addGenotypeGVCFs(inputGvcfs, outputFile)
if (!samples.isEmpty) {
- if (samples.size > 1) addSelectVariants(outputFile, samples, outputDir + "samples/", "all")
- for (sample <- samples) addSelectVariants(outputFile, List(sample), outputDir + "samples/", sample)
+ if (samples.size > 1) addSelectVariants(outputFile, samples, new File(outputDir, "samples/"), "all")
+ for (sample <- samples) addSelectVariants(outputFile, List(sample), new File(outputDir, "samples/"), sample)
}
}
@@ -52,8 +51,8 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
return genotypeGVCFs.out
}
- def addSelectVariants(inputFile: File, samples: List[String], outputDir: String, name: String) {
- val selectVariants = SelectVariants(this, inputFile, outputDir + name + ".vcf.gz")
+ def addSelectVariants(inputFile: File, samples: List[String], outputDir: File, name: String) {
+ val selectVariants = SelectVariants(this, inputFile, new File(outputDir, name + ".vcf.gz"))
selectVariants.excludeNonVariants = true
for (sample <- samples) selectVariants.sample_name :+= sample
add(selectVariants)
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
index c76139133f23cf434884ad69ccc9dafc69b2cac9..b65eb6abaec460f3633d2da148bafb39bc0d49eb 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
@@ -9,6 +9,7 @@ import nl.lumc.sasc.biopet.core.MultiSampleQScript
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import htsjdk.samtools.SamReaderFactory
+import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import scala.collection.JavaConversions._
import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, CombineGVCFs }
import nl.lumc.sasc.biopet.extensions.picard.AddOrReplaceReadGroups
@@ -35,7 +36,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
var jointGenotyping: Boolean = config("joint_genotyping", default = false)
var singleSampleCalling = config("single_sample_calling", default = true)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
var useAllelesOption: Boolean = config("use_alleles_option", default = false)
val externalGvcfs = config("external_gvcfs_files", default = Nil).asFileList
@@ -46,12 +47,13 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
val mapping = new Mapping(qscript)
mapping.sampleId = sampleId
mapping.libId = libId
- mapping.outputDir = libDir + "/variantcalling/"
+ mapping.outputDir = libDir
/** Library variantcalling */
val gatkVariantcalling = new GatkVariantcalling(qscript)
+ gatkVariantcalling.doublePreProces = false
gatkVariantcalling.sampleID = sampleId
- gatkVariantcalling.outputDir = libDir
+ gatkVariantcalling.outputDir = new File(libDir, "variantcalling")
protected def addJobs(): Unit = {
val bamFile: Option[File] = if (config.contains("R1")) {
@@ -112,7 +114,6 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
if (bamFile.isDefined) {
gatkVariantcalling.inputBams = List(bamFile.get)
gatkVariantcalling.variantcalling = config("library_variantcalling", default = false)
- gatkVariantcalling.preProcesBams = true
gatkVariantcalling.init
gatkVariantcalling.biopetScript
addAll(gatkVariantcalling.functions)
@@ -123,7 +124,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
/** sample variantcalling */
val gatkVariantcalling = new GatkVariantcalling(qscript)
gatkVariantcalling.sampleID = sampleId
- gatkVariantcalling.outputDir = sampleDir + "/variantcalling/"
+ gatkVariantcalling.outputDir = new File(sampleDir, "variantcalling/")
protected def addJobs(): Unit = {
addPerLibJobs()
@@ -136,12 +137,12 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
gatkVariantcalling.init
gatkVariantcalling.biopetScript
addAll(gatkVariantcalling.functions)
+
+ gatkVariantcalling.inputBams.foreach(x => addAll(Bam2Wig(qscript, x).functions))
}
}
def init() {
- if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
- else if (!outputDir.endsWith("/")) outputDir += "/"
}
val multisampleVariantcalling = new GatkVariantcalling(this) {
@@ -155,7 +156,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
def addMultiSampleJobs(): Unit = {
val gvcfFiles: List[File] = if (mergeGvcfs && externalGvcfs.size + samples.size > 1) {
- val newFile = outputDir + "merged.gvcf.vcf.gz"
+ val newFile = new File(outputDir, "merged.gvcf.vcf.gz")
add(CombineGVCFs(this, externalGvcfs ++ samples.map(_._2.gatkVariantcalling.scriptOutput.gvcfFile), newFile))
List(newFile)
} else externalGvcfs ++ samples.map(_._2.gatkVariantcalling.scriptOutput.gvcfFile)
@@ -164,7 +165,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
if (jointGenotyping) {
val gatkGenotyping = new GatkGenotyping(this)
gatkGenotyping.inputGvcfs = gvcfFiles
- gatkGenotyping.outputDir = outputDir + "genotyping/"
+ gatkGenotyping.outputDir = new File(outputDir, "genotyping")
gatkGenotyping.init
gatkGenotyping.biopetScript
addAll(gatkGenotyping.functions)
@@ -182,7 +183,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
}
if (gatkVariantcalling.useMpileup) {
- val cvRaw = CombineVariants(this, allRawVcfFiles.toList, outputDir + "variantcalling/multisample.raw.vcf.gz")
+ val cvRaw = CombineVariants(this, allRawVcfFiles.toList, new File(outputDir, "variantcalling/multisample.raw.vcf.gz"))
add(cvRaw)
gatkVariantcalling.rawVcfInput = cvRaw.out
}
@@ -190,7 +191,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
multisampleVariantcalling.preProcesBams = false
multisampleVariantcalling.doublePreProces = false
multisampleVariantcalling.inputBams = allBamfiles.toList
- multisampleVariantcalling.outputDir = outputDir + "variantcalling"
+ multisampleVariantcalling.outputDir = new File(outputDir, "variantcalling")
multisampleVariantcalling.outputName = "multisample"
multisampleVariantcalling.init
multisampleVariantcalling.biopetScript
@@ -200,7 +201,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
val recalibration = new GatkVariantRecalibration(this)
recalibration.inputVcf = multisampleVariantcalling.scriptOutput.finalVcfFile
recalibration.bamFiles = allBamfiles
- recalibration.outputDir = outputDir + "recalibration/"
+ recalibration.outputDir = new File(outputDir, "recalibration")
recalibration.init
recalibration.biopetScript
}
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
index 409d83c7168891a4df5f100c711e8a0a1d0fc2b2..0e057f4a2cdf5131775d453edc816f00f37c3302 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
@@ -26,9 +26,7 @@ class GatkVariantRecalibration(val root: Configurable) extends QScript with Biop
var outputVcf: File = _
def init() {
- if (inputVcf == null) throw new IllegalStateException("Missing Output directory on gatk module")
- if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
- else if (!outputDir.endsWith("/")) outputDir += "/"
+ require(inputVcf != null, "Missing Output directory on gatk module")
}
def biopetScript() {
@@ -37,7 +35,7 @@ class GatkVariantRecalibration(val root: Configurable) extends QScript with Biop
vcfFile = addIndelVariantRecalibrator(vcfFile, outputDir)
}
- def addSnpVariantRecalibrator(inputVcf: File, dir: String): File = {
+ def addSnpVariantRecalibrator(inputVcf: File, dir: File): File = {
val snpRecal = VariantRecalibrator(this, inputVcf, swapExt(dir, inputVcf, ".vcf", ".indel.recal"),
swapExt(dir, inputVcf, ".vcf", ".indel.tranches"), indel = false)
if (!snpRecal.resource.isEmpty) {
@@ -54,7 +52,7 @@ class GatkVariantRecalibration(val root: Configurable) extends QScript with Biop
}
}
- def addIndelVariantRecalibrator(inputVcf: File, dir: String): File = {
+ def addIndelVariantRecalibrator(inputVcf: File, dir: File): File = {
val indelRecal = VariantRecalibrator(this, inputVcf, swapExt(dir, inputVcf, ".vcf", ".indel.recal"),
swapExt(dir, inputVcf, ".vcf", ".indel.tranches"), indel = true)
if (!indelRecal.resource.isEmpty) {
@@ -71,7 +69,7 @@ class GatkVariantRecalibration(val root: Configurable) extends QScript with Biop
}
}
- def addVariantAnnotator(inputvcf: File, bamfiles: List[File], dir: String): File = {
+ def addVariantAnnotator(inputvcf: File, bamfiles: List[File], dir: File): File = {
val variantAnnotator = VariantAnnotator(this, inputvcf, bamfiles, swapExt(dir, inputvcf, ".vcf", ".anotated.vcf"))
add(variantAnnotator)
return variantAnnotator.out
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
index 8bac4aaf68c33a245da877d460bc26abb9ebe564..8e89a84fd7ab7f042a574cf61259638e2a647400 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
@@ -7,6 +7,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import java.io.File
+import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.tools.{ VcfStats, MpileupToVcf, VcfFilter, MergeAlleles }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.gatk.{ AnalyzeCovariates, BaseRecalibrator, GenotypeGVCFs, HaplotypeCaller, IndelRealigner, PrintReads, RealignerTargetCreator, SelectVariants, CombineVariants, UnifiedGenotyper }
@@ -30,7 +31,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
var rawVcfInput: File = _
@Argument(doc = "Reference", shortName = "R", required = false)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Argument(doc = "OutputName", required = false)
var outputName: String = _
@@ -38,12 +39,12 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
@Argument(doc = "Sample name", required = false)
var sampleID: String = _
- var preProcesBams: Option[Boolean] = config("pre_proces_bams", default = true)
+ var preProcesBams: Boolean = config("pre_proces_bams", default = true)
var variantcalling: Boolean = true
- var doublePreProces: Option[Boolean] = config("double_pre_proces", default = true)
- var useHaplotypecaller: Option[Boolean] = config("use_haplotypecaller", default = true)
- var useUnifiedGenotyper: Option[Boolean] = config("use_unifiedgenotyper", default = false)
- var useAllelesOption: Option[Boolean] = config("use_alleles_option", default = false)
+ var doublePreProces: Boolean = config("double_pre_proces", default = true)
+ var useHaplotypecaller: Boolean = config("use_haplotypecaller", default = true)
+ var useUnifiedGenotyper: Boolean = config("use_unifiedgenotyper", default = false)
+ var useAllelesOption: Boolean = config("use_alleles_option", default = false)
var useMpileup: Boolean = config("use_mpileup", default = true)
var useIndelRealigner: Boolean = config("use_indel_realign", default = true)
var useBaseRecalibration: Boolean = config("use_base_recalibration", default = true)
@@ -51,8 +52,6 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
def init() {
if (outputName == null && sampleID != null) outputName = sampleID
else if (outputName == null) outputName = config("output_name", default = "noname")
- if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
- else if (!outputDir.endsWith("/")) outputDir += "/"
val baseRecalibrator = new BaseRecalibrator(this)
if (preProcesBams && useBaseRecalibration && baseRecalibrator.knownSites.isEmpty) {
@@ -62,69 +61,80 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
}
private def doublePreProces(files: List[File]): List[File] = {
- if (files.size == 1) return files
if (files.isEmpty) throw new IllegalStateException("Files can't be empty")
- if (!doublePreProces.get) return files
- val markDup = MarkDuplicates(this, files, new File(outputDir + outputName + ".dedup.bam"))
- markDup.isIntermediate = useIndelRealigner
- add(markDup)
- if (useIndelRealigner) {
- List(addIndelRealign(markDup.output, outputDir, isIntermediate = false))
+ else if (!doublePreProces) files
+ else if (files.size == 1) {
+ val bamFile = new File(outputDir, files.head.getName)
+ if (bamFile != files.head) {
+ val oldIndex: File = files.head.getAbsolutePath.stripSuffix(".bam") + ".bai"
+ val newIndex: File = bamFile.getAbsolutePath.stripSuffix(".bam") + ".bai"
+ add(Ln(this, oldIndex, newIndex))
+
+ val bamLn = Ln(this, files.head, bamFile)
+ bamLn.deps :+= newIndex
+ add(bamLn)
+ }
+ List(bamFile)
} else {
- List(markDup.output)
+ val markDup = MarkDuplicates(this, files, new File(outputDir + outputName + ".dedup.bam"))
+ markDup.isIntermediate = useIndelRealigner
+ add(markDup)
+ if (useIndelRealigner) {
+ List(addIndelRealign(markDup.output, outputDir, isIntermediate = false))
+ } else {
+ List(markDup.output)
+ }
}
}
def biopetScript() {
- scriptOutput.bamFiles = if (preProcesBams.get) {
- var bamFiles: List[File] = Nil
- for (inputBam <- inputBams) {
- var bamFile = inputBam
- if (useIndelRealigner) {
- bamFile = addIndelRealign(bamFile, outputDir, isIntermediate = useBaseRecalibration)
- }
- if (useBaseRecalibration) {
- bamFile = addBaseRecalibrator(bamFile, outputDir, isIntermediate = bamFiles.size > 1)
+ scriptOutput.bamFiles = {
+ doublePreProces(if (preProcesBams) {
+ for (inputBam <- inputBams) yield {
+ var bamFile = inputBam
+ if (useIndelRealigner)
+ bamFile = addIndelRealign(bamFile, outputDir, isIntermediate = useBaseRecalibration)
+ if (useBaseRecalibration)
+ bamFile = addBaseRecalibrator(bamFile, outputDir, isIntermediate = inputBams.size > 1)
+ bamFile
}
- bamFiles :+= bamFile
- }
- doublePreProces(bamFiles)
- } else if (inputBams.size > 1 && doublePreProces.get) {
- doublePreProces(inputBams)
- } else inputBams
+ } else {
+ inputBams
+ })
+ }
if (variantcalling) {
var mergBuffer: SortedMap[String, File] = SortedMap()
def mergeList = mergBuffer map { case (key, file) => TaggedFile(removeNoneVariants(file), "name=" + key) }
- if (sampleID != null && (useHaplotypecaller.get || config("joint_genotyping", default = false).asBoolean)) {
+ if (sampleID != null && (useHaplotypecaller || config("joint_genotyping", default = false).asBoolean)) {
val hcGvcf = new HaplotypeCaller(this)
hcGvcf.useGvcf
hcGvcf.input_file = scriptOutput.bamFiles
- hcGvcf.out = outputDir + outputName + ".hc.discovery.gvcf.vcf.gz"
+ hcGvcf.out = new File(outputDir, outputName + ".hc.discovery.gvcf.vcf.gz")
add(hcGvcf)
scriptOutput.gvcfFile = hcGvcf.out
}
- if (useHaplotypecaller.get) {
+ if (useHaplotypecaller) {
if (sampleID != null) {
- val genotypeGVCFs = GenotypeGVCFs(this, List(scriptOutput.gvcfFile), outputDir + outputName + ".hc.discovery.vcf.gz")
+ val genotypeGVCFs = GenotypeGVCFs(this, List(scriptOutput.gvcfFile), new File(outputDir, outputName + ".hc.discovery.vcf.gz"))
add(genotypeGVCFs)
scriptOutput.hcVcfFile = genotypeGVCFs.out
} else {
val hcGvcf = new HaplotypeCaller(this)
hcGvcf.input_file = scriptOutput.bamFiles
- hcGvcf.out = outputDir + outputName + ".hc.discovery.vcf.gz"
+ hcGvcf.out = new File(outputDir, outputName + ".hc.discovery.vcf.gz")
add(hcGvcf)
scriptOutput.hcVcfFile = hcGvcf.out
}
mergBuffer += ("1.HC-Discovery" -> scriptOutput.hcVcfFile)
}
- if (useUnifiedGenotyper.get) {
+ if (useUnifiedGenotyper) {
val ugVcf = new UnifiedGenotyper(this)
ugVcf.input_file = scriptOutput.bamFiles
- ugVcf.out = outputDir + outputName + ".ug.discovery.vcf.gz"
+ ugVcf.out = new File(outputDir, outputName + ".ug.discovery.vcf.gz")
add(ugVcf)
scriptOutput.ugVcfFile = ugVcf.out
mergBuffer += ("2.UG-Discovery" -> scriptOutput.ugVcfFile)
@@ -136,7 +146,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
val m2v = new MpileupToVcf(this)
m2v.inputBam = scriptOutput.bamFiles.head
m2v.sample = sampleID
- m2v.output = outputDir + outputName + ".raw.vcf"
+ m2v.output = new File(outputDir, outputName + ".raw.vcf")
add(m2v)
scriptOutput.rawVcfFile = m2v.output
@@ -148,7 +158,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
), super.defaults)
}
vcfFilter.inputVcf = m2v.output
- vcfFilter.outputVcf = this.swapExt(outputDir, m2v.output, ".vcf", ".filter.vcf.gz")
+ vcfFilter.outputVcf = swapExt(outputDir, m2v.output, ".vcf", ".filter.vcf.gz")
add(vcfFilter)
scriptOutput.rawFilterVcfFile = vcfFilter.outputVcf
} else if (rawVcfInput != null) scriptOutput.rawFilterVcfFile = rawVcfInput
@@ -156,15 +166,15 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
}
// Allele mode
- if (useAllelesOption.get) {
+ if (useAllelesOption) {
val mergeAlleles = MergeAlleles(this, mergeList.toList, outputDir + "raw.allele__temp_only.vcf.gz")
mergeAlleles.isIntermediate = true
add(mergeAlleles)
- if (useHaplotypecaller.get) {
+ if (useHaplotypecaller) {
val hcAlleles = new HaplotypeCaller(this)
hcAlleles.input_file = scriptOutput.bamFiles
- hcAlleles.out = outputDir + outputName + ".hc.allele.vcf.gz"
+ hcAlleles.out = new File(outputDir, outputName + ".hc.allele.vcf.gz")
hcAlleles.alleles = mergeAlleles.output
hcAlleles.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
add(hcAlleles)
@@ -172,10 +182,10 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
mergBuffer += ("3.HC-alleles" -> hcAlleles.out)
}
- if (useUnifiedGenotyper.get) {
+ if (useUnifiedGenotyper) {
val ugAlleles = new UnifiedGenotyper(this)
ugAlleles.input_file = scriptOutput.bamFiles
- ugAlleles.out = outputDir + outputName + ".ug.allele.vcf.gz"
+ ugAlleles.out = new File(outputDir, outputName + ".ug.allele.vcf.gz")
ugAlleles.alleles = mergeAlleles.output
ugAlleles.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
add(ugAlleles)
@@ -194,32 +204,32 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
sv.out
}
- val cvFinal = CombineVariants(this, mergeList.toList, outputDir + outputName + ".final.vcf.gz")
+ val cvFinal = CombineVariants(this, mergeList.toList, new File(outputDir, outputName + ".final.vcf.gz"))
cvFinal.genotypemergeoption = org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.GenotypeMergeType.UNSORTED
add(cvFinal)
val vcfStats = new VcfStats(this)
vcfStats.input = cvFinal.out
- vcfStats.setOutputDir(outputDir + File.separator + "vcfstats")
+ vcfStats.setOutputDir(new File(outputDir, "vcfstats"))
add(vcfStats)
scriptOutput.finalVcfFile = cvFinal.out
}
}
- def addIndelRealign(inputBam: File, dir: String, isIntermediate: Boolean = true): File = {
+ def addIndelRealign(inputBam: File, dir: File, isIntermediate: Boolean = true): File = {
val realignerTargetCreator = RealignerTargetCreator(this, inputBam, dir)
realignerTargetCreator.isIntermediate = true
add(realignerTargetCreator)
- val indelRealigner = IndelRealigner.apply(this, inputBam, realignerTargetCreator.out, dir)
+ val indelRealigner = IndelRealigner(this, inputBam, realignerTargetCreator.out, dir)
indelRealigner.isIntermediate = isIntermediate
add(indelRealigner)
return indelRealigner.o
}
- def addBaseRecalibrator(inputBam: File, dir: String, isIntermediate: Boolean = false): File = {
+ def addBaseRecalibrator(inputBam: File, dir: File, isIntermediate: Boolean = false): File = {
val baseRecalibrator = BaseRecalibrator(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal"))
if (baseRecalibrator.knownSites.isEmpty) {
diff --git a/protected/biopet-gatk-pipelines/src/test/resources/log4j.properties b/protected/biopet-gatk-pipelines/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/protected/biopet-gatk-pipelines/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/protected/biopet-protected-package/BiopetProtectedPackage.iml b/protected/biopet-protected-package/BiopetProtectedPackage.iml
deleted file mode 100644
index f50e84ce7acbbabc8a93e9fc20dcc0c50ed33298..0000000000000000000000000000000000000000
--- a/protected/biopet-protected-package/BiopetProtectedPackage.iml
+++ /dev/null
@@ -1,103 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="false">
- <output url="file://$MODULE_DIR$/target/classes" />
- <output-test url="file://$MODULE_DIR$/target/test-classes" />
- <content url="file://$MODULE_DIR$">
- <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
- <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
- <excludeFolder url="file://$MODULE_DIR$/target" />
- </content>
- <orderEntry type="inheritedJdk" />
- <orderEntry type="sourceFolder" forTests="false" />
- <orderEntry type="module" module-name="BiopetFramework" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" />
- <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" />
- <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" />
- <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" />
- <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" />
- <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" />
- <orderEntry type="module-library">
- <library name="Maven: com.sun:tools:1.4.2">
- <CLASSES>
- <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" />
- </CLASSES>
- <JAVADOC />
- <SOURCES />
- </library>
- </orderEntry>
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" />
- <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" />
- <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" />
- <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" />
- <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" />
- <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" />
- <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" />
- <orderEntry type="module-library">
- <library name="Maven: com.sun:tools.jar:1.5">
- <CLASSES>
- <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" />
- </CLASSES>
- <JAVADOC />
- <SOURCES />
- </library>
- </orderEntry>
- <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" />
- <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" />
- <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" />
- <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" />
- <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" />
- <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" />
- <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
- <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" />
- <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
- <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" />
- <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" />
- <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" />
- <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" />
- <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" />
- <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" />
- <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" />
- <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" />
- <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
- <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" />
- <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" />
- <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" />
- <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" />
- <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" />
- <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" />
- <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" />
- <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" />
- <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" />
- <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" />
- <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" />
- <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" />
- <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" />
- <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" />
- <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" />
- <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" />
- <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" />
- <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
- <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" />
- <orderEntry type="module" module-name="BiopetPublicPackage" />
- <orderEntry type="module" module-name="Flexiprep" />
- <orderEntry type="module" module-name="Mapping" />
- <orderEntry type="module" module-name="BamMetrics" />
- <orderEntry type="module" module-name="Gentrap" />
- <orderEntry type="module" module-name="Sage" />
- <orderEntry type="module" module-name="Yamsvp" />
- <orderEntry type="module" module-name="Toucan" />
- <orderEntry type="module" module-name="BiopetGatkPipelines" />
- <orderEntry type="module" module-name="BiopetGatkExtensions" />
- <orderEntry type="module" module-name="Basty" />
- </component>
-</module>
\ No newline at end of file
diff --git a/protected/biopet-protected-package/src/test/resources/log4j.properties b/protected/biopet-protected-package/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/protected/biopet-protected-package/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/protected/log4j.properties b/protected/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/protected/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/protected/src/src/test/resources/log4j.properties b/protected/src/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/protected/src/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/public/Biopet.iml b/public/Biopet.iml
deleted file mode 100644
index 9120ea623670da6fa98d7f004662ab238a4fa936..0000000000000000000000000000000000000000
--- a/public/Biopet.iml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="false">
- <output url="file://$MODULE_DIR$/target/classes" />
- <output-test url="file://$MODULE_DIR$/target/test-classes" />
- <content url="file://$MODULE_DIR$">
- <excludeFolder url="file://$MODULE_DIR$/target" />
- </content>
- <orderEntry type="inheritedJdk" />
- <orderEntry type="sourceFolder" forTests="false" />
- </component>
-</module>
\ No newline at end of file
diff --git a/public/bam2wig/.gitignore b/public/bam2wig/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..a6f89c2da7a029afa02b6e7a2bf80ad34958a311
--- /dev/null
+++ b/public/bam2wig/.gitignore
@@ -0,0 +1 @@
+/target/
\ No newline at end of file
diff --git a/public/bam2wig/pom.xml b/public/bam2wig/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..6a20ded1b5f9ff98c85f5a6d49a24db6534f670d
--- /dev/null
+++ b/public/bam2wig/pom.xml
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>Bam2Wig</artifactId>
+ <packaging>jar</packaging>
+
+ <parent>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>Biopet</artifactId>
+ <version>0.3.0-DEV</version>
+ <relativePath>../</relativePath>
+ </parent>
+
+ <inceptionYear>2014</inceptionYear>
+ <name>Bam2Wig</name>
+
+ <dependencies>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetFramework</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+
+</project>
\ No newline at end of file
diff --git a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
new file mode 100644
index 0000000000000000000000000000000000000000..8c1f543bf551d7b828bf17ea4afda47c1bf036dd
--- /dev/null
+++ b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
@@ -0,0 +1,55 @@
+package nl.lumc.sasc.biopet.pipelines.bamtobigwig
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.extensions.WigToBigWig
+import nl.lumc.sasc.biopet.extensions.igvtools.IGVToolsCount
+import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+
+/**
+ * Created by pjvan_thof on 1/29/15.
+ */
+class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
+ def this() = this(null)
+
+ @Input(doc = "Input bam file", required = true)
+ var bamFile: File = null
+
+ def init(): Unit = {
+ }
+
+ def biopetScript(): Unit = {
+ val bs = new BamToChromSizes(this)
+ bs.bamFile = bamFile
+ bs.chromSizesFile = bamFile.getAbsoluteFile + ".chrom.sizes"
+ bs.isIntermediate = true
+ add(bs)
+
+ val igvCount = new IGVToolsCount(this)
+ igvCount.input = bamFile
+ igvCount.genomeChromSizes = bs.chromSizesFile
+ igvCount.wig = Some(swapExt(outputDir, bamFile, ".bam", ".wig"))
+ igvCount.tdf = Some(swapExt(outputDir, bamFile, ".bam", ".tdf"))
+ add(igvCount)
+
+ val wigToBigWig = new WigToBigWig(this)
+ wigToBigWig.inputWigFile = igvCount.wig.get
+ wigToBigWig.inputChromSizesFile = bs.chromSizesFile
+ wigToBigWig.outputBigWig = swapExt(outputDir, bamFile, ".bam", ".bigwig")
+ add(wigToBigWig)
+ }
+}
+
+object Bam2Wig extends PipelineCommand {
+ def apply(root: Configurable, bamFile: File): Bam2Wig = {
+ val bamToBigWig = new Bam2Wig(root)
+ bamToBigWig.outputDir = bamFile.getParentFile
+ bamToBigWig.bamFile = bamFile
+ bamToBigWig.init()
+ bamToBigWig.biopetScript()
+ bamToBigWig
+ }
+}
\ No newline at end of file
diff --git a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
new file mode 100644
index 0000000000000000000000000000000000000000..5ed1fae9f34191b7394a8dd09b78432ea8a2bdd9
--- /dev/null
+++ b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
@@ -0,0 +1,30 @@
+package nl.lumc.sasc.biopet.pipelines.bamtobigwig
+
+import java.io.{ PrintWriter, File }
+
+import htsjdk.samtools.SamReaderFactory
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.queue.function.InProcessFunction
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+import scala.collection.JavaConversions._
+
+/**
+ * Created by pjvan_thof on 1/29/15.
+ */
+class BamToChromSizes(val root: Configurable) extends InProcessFunction with Configurable {
+ @Input
+ var bamFile: File = _
+
+ @Output
+ var chromSizesFile: File = _
+
+ def run(): Unit = {
+ val bamReader = SamReaderFactory.makeDefault().open(bamFile)
+ val writer = new PrintWriter(chromSizesFile)
+ for (ref <- bamReader.getFileHeader.getSequenceDictionary.getSequences) {
+ writer.println(ref.getSequenceName + "\t" + ref.getSequenceLength)
+ }
+ bamReader.close()
+ writer.close
+ }
+}
diff --git a/public/bam2wig/src/test/resources/log4j.properties b/public/bam2wig/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/public/bam2wig/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/public/bammetrics/BamMetrics.iml b/public/bammetrics/BamMetrics.iml
deleted file mode 100644
index dc0afbee2ccf2f185458a930863b52ade6962739..0000000000000000000000000000000000000000
--- a/public/bammetrics/BamMetrics.iml
+++ /dev/null
@@ -1,92 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="false">
- <output url="file://$MODULE_DIR$/target/classes" />
- <output-test url="file://$MODULE_DIR$/target/test-classes" />
- <content url="file://$MODULE_DIR$">
- <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
- <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
- <excludeFolder url="file://$MODULE_DIR$/target" />
- </content>
- <orderEntry type="inheritedJdk" />
- <orderEntry type="sourceFolder" forTests="false" />
- <orderEntry type="module" module-name="BiopetFramework" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" />
- <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" />
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- <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" />
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- <library name="Maven: com.sun:tools:1.4.2">
- <CLASSES>
- <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" />
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- <JAVADOC />
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- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" />
- <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" />
- <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" />
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- <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" />
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- <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" />
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- <SOURCES />
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- <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" />
- <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" />
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- <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" />
- <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" />
- <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
- <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" />
- </component>
-</module>
\ No newline at end of file
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index a23486320609a0fa1563c3d5b21358cf70eb5d80..5a17ea0d95d43b2ba57d456821f89a60d5135c6a 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -41,8 +41,6 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
var wholeGenome = false
def init() {
- if (outputDir == null) throw new IllegalStateException("Missing Output directory on BamMetrics module")
- else if (!outputDir.endsWith("/")) outputDir += "/"
if (config.contains("target_bed")) {
for (file <- config("target_bed").asList) {
bedFiles +:= new File(file.toString)
@@ -63,7 +61,7 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
add(BedToInterval(this, baitBedFile, inputBam, outputDir), true)
for (bedFile <- bedFiles) {
- val targetDir = outputDir + bedFile.getName.stripSuffix(".bed") + "/"
+ val targetDir = new File(outputDir, bedFile.getName.stripSuffix(".bed"))
val targetInterval = BedToInterval(this, bedFile, inputBam, targetDir)
add(targetInterval, true)
add(CalculateHsMetrics(this, inputBam, if (baitIntervalFile != null) baitIntervalFile
@@ -71,12 +69,12 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
val strictOutputBam = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.bam")
add(BedtoolsIntersect(this, inputBam, bedFile, strictOutputBam, minOverlap = config("strictintersectoverlap", default = 1.0)), true)
- add(SamtoolsFlagstat(this, strictOutputBam))
+ add(SamtoolsFlagstat(this, strictOutputBam, targetDir))
add(BiopetFlagstat(this, strictOutputBam, targetDir))
val looseOutputBam = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.bam")
add(BedtoolsIntersect(this, inputBam, bedFile, looseOutputBam, minOverlap = config("looseintersectoverlap", default = 0.01)), true)
- add(SamtoolsFlagstat(this, looseOutputBam))
+ add(SamtoolsFlagstat(this, looseOutputBam, targetDir))
add(BiopetFlagstat(this, looseOutputBam, targetDir))
val coverageFile = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".coverage")
@@ -87,7 +85,7 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
}
object BamMetrics extends PipelineCommand {
- def apply(root: Configurable, bamFile: File, outputDir: String): BamMetrics = {
+ def apply(root: Configurable, bamFile: File, outputDir: File): BamMetrics = {
val bamMetrics = new BamMetrics(root)
bamMetrics.inputBam = bamFile
bamMetrics.outputDir = outputDir
diff --git a/public/bammetrics/src/test/resources/log4j.properties b/public/bammetrics/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/public/bammetrics/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/public/biopet-framework/BiopetFramework.iml b/public/biopet-framework/BiopetFramework.iml
deleted file mode 100644
index 042a396425eab9346a4c30774b1d5c811cddad04..0000000000000000000000000000000000000000
--- a/public/biopet-framework/BiopetFramework.iml
+++ /dev/null
@@ -1,101 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="false">
- <output url="file://$MODULE_DIR$/target/classes" />
- <output-test url="file://$MODULE_DIR$/target/test-classes" />
- <content url="file://$MODULE_DIR$">
- <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
- <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
- <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
- <sourceFolder url="file://$MODULE_DIR$/src/test/scala" isTestSource="true" />
- <excludeFolder url="file://$MODULE_DIR$/target" />
- </content>
- <orderEntry type="inheritedJdk" />
- <orderEntry type="sourceFolder" forTests="false" />
- <orderEntry type="library" scope="TEST" name="Maven: org.testng:testng:6.8" level="project" />
- <orderEntry type="library" name="Maven: junit:junit:4.10" level="project" />
- <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.1" level="project" />
- <orderEntry type="library" scope="TEST" name="Maven: org.beanshell:bsh:2.0b4" level="project" />
- <orderEntry type="library" scope="TEST" name="Maven: com.beust:jcommander:1.27" level="project" />
- <orderEntry type="library" scope="TEST" name="Maven: org.yaml:snakeyaml:1.6" level="project" />
- <orderEntry type="library" scope="TEST" name="Maven: org.mockito:mockito-all:1.9.5" level="project" />
- <orderEntry type="library" scope="TEST" name="Maven: org.scalatest:scalatest_2.11:2.2.1" level="project" />
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- <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" />
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- <CLASSES>
- <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" />
- </CLASSES>
- <JAVADOC />
- <SOURCES />
- </library>
- </orderEntry>
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" />
- <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" />
- <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" />
- <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" />
- <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" />
- <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" />
- <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" />
- <orderEntry type="module-library">
- <library name="Maven: com.sun:tools.jar:1.5">
- <CLASSES>
- <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" />
- </CLASSES>
- <JAVADOC />
- <SOURCES />
- </library>
- </orderEntry>
- <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" />
- <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" />
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- <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" />
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- <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
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- <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" />
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- <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" />
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- <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" />
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- <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" />
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- <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" />
- <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" />
- <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" />
- <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" />
- <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" />
- <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
- <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" />
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-</module>
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
index 4ec1a0af9f58c9cce28aa321c3c042b8c87dd194..b73f76c7bb72ba4a7022c3eba1381e3f85324fda 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
@@ -15,8 +15,21 @@
*/
package nl.lumc.sasc.biopet.core
+/**
+ * This class is for commandline programs where the executable is a non JVM based program
+ */
abstract class BiopetCommandLineFunction extends BiopetCommandLineFunctionTrait {
+ /**
+ * This function needs to be implemented to define the command that is executed
+ * @return Command to run
+ */
protected def cmdLine: String
+
+ /**
+ * implementing a final version of the commandLine from org.broadinstitute.gatk.queue.function.CommandLineFunction
+ * User needs to implement cmdLine instead
+ * @return Command to run
+ */
final def commandLine: String = {
preCmdInternal
val cmd = cmdLine
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index 4a5b25f7a5b816fe32ad39897a334a6e13fe1eda..944dee43fa5fae667cad5e08a05ae4ce9d5f8fbe 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -25,33 +25,40 @@ import scala.util.matching.Regex
import java.io.FileInputStream
import java.security.MessageDigest
+/**
+ * Biopet command line trait to auto check executable and cluster values
+ */
trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurable {
analysisName = configName
@Input(doc = "deps", required = false)
var deps: List[File] = Nil
- @Argument(doc = "Threads", required = false)
var threads = 0
val defaultThreads = 1
- @Argument(doc = "Vmem", required = false)
var vmem: Option[String] = None
val defaultVmem: String = ""
-
- @Argument(doc = "Executable", required = false)
var executable: String = _
- protected[core] def beforeCmd {
- }
+ /**
+ * Can override this method. This is executed just before the job is ready to run.
+ * Can check on run time files from pipeline here
+ */
+ protected[core] def beforeCmd {}
- protected[core] def afterGraph {
- }
+ /**
+ * Can override this method. This is executed after the script is done en queue starts to generate the graph
+ */
+ protected[core] def beforeGraph {}
+ /**
+ * Set default output file, threads and vmem for current job
+ */
override def freezeFieldValues() {
- checkExecutable
- afterGraph
- if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getParent + "/." + firstOutput.getName + "." + configName + ".out")
+ preProcesExecutable
+ beforeGraph
+ if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getAbsoluteFile.getParent, "." + firstOutput.getName + "." + configName + ".out")
if (threads == 0) threads = getThreads(defaultThreads)
if (threads > 1) nCoresRequest = Option(threads)
@@ -66,7 +73,10 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
super.freezeFieldValues()
}
- protected def checkExecutable {
+ /**
+ * Checks executable. Follow full CanonicalPath, checks if it is existing and do a md5sum on it to store in job report
+ */
+ protected[core] def preProcesExecutable {
if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
try if (executable != null) {
if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable)) {
@@ -79,8 +89,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
val file = new File(executable)
executable = file.getCanonicalPath
} else {
- logger.error("executable: '" + executable + "' not found, please check config")
- throw new QException("executable: '" + executable + "' not found, please check config")
+ BiopetQScript.addError("executable: '" + executable + "' not found, please check config")
}
BiopetCommandLineFunctionTrait.executableCache += oldExecutable -> executable
BiopetCommandLineFunctionTrait.executableCache += executable -> executable
@@ -101,25 +110,42 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executable skipped: " + ioe)
}
}
- val md5 = BiopetCommandLineFunctionTrait.executableMd5Cache(executable)
- if (md5 == null) addJobReportBinding("md5sum_exe", md5)
- else addJobReportBinding("md5sum_exe", "None")
+ val md5 = BiopetCommandLineFunctionTrait.executableMd5Cache.get(executable)
+ addJobReportBinding("md5sum_exe", md5.getOrElse("None"))
}
+ /**
+ * executes checkExecutable method and fill job report
+ */
final protected def preCmdInternal {
- checkExecutable
+ preProcesExecutable
beforeCmd
- addJobReportBinding("cores", if (nCoresRequest.get.toInt > 0) nCoresRequest.get.toInt else 1)
+ addJobReportBinding("cores", nCoresRequest match {
+ case Some(n) if n > 0 => n
+ case _ => 1
+ })
addJobReportBinding("version", getVersion)
}
+ /**
+ * Command to get version of executable
+ * @return
+ */
protected def versionCommand: String = null
+
+ /** Regex to get version from version command output */
protected val versionRegex: Regex = null
- protected val versionExitcode = List(0) // Can select multiple
+
+ /** Allowed exit codes for the version command */
+ protected val versionExitcode = List(0)
+
+ /** Executes the version command */
private def getVersionInternal: String = {
if (versionCommand == null || versionRegex == null) return "N/A"
+ val exe = new File(versionCommand.trim.split(" ")(0))
+ if (!exe.exists()) return "N/A"
val stdout = new StringBuffer()
val stderr = new StringBuffer()
def outputLog = "Version command: \n" + versionCommand +
@@ -140,12 +166,20 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
return "N/A"
}
+ /** Get version from cache otherwise execute the version command */
def getVersion: String = {
+ if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable))
+ preProcesExecutable
if (!BiopetCommandLineFunctionTrait.versionCache.contains(executable))
BiopetCommandLineFunctionTrait.versionCache += executable -> getVersionInternal
return BiopetCommandLineFunctionTrait.versionCache(executable)
}
+ /**
+ * Get threads from config
+ * @param default default when not found in config
+ * @return number of threads
+ */
def getThreads(default: Int): Int = {
val maxThreads: Int = config("maxthreads", default = 8)
val threads: Int = config("threads", default = default)
@@ -153,6 +187,12 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
else return maxThreads
}
+ /**
+ * Get threads from config
+ * @param default default when not found in config
+ * @param module Module when this is difrent from default
+ * @return number of threads
+ */
def getThreads(default: Int, module: String): Int = {
val maxThreads: Int = config("maxthreads", default = 8, submodule = module)
val threads: Int = config("threads", default = default, submodule = module)
@@ -161,9 +201,12 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
}
}
+/**
+ * stores global caches
+ */
object BiopetCommandLineFunctionTrait {
import scala.collection.mutable.Map
private val versionCache: Map[String, String] = Map()
private val executableMd5Cache: Map[String, String] = Map()
private val executableCache: Map[String, String] = Map()
-}
\ No newline at end of file
+}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
index ed3a1d99c1ccd33d8d5b128aaada5144b1a369e2..b0657e369afa46d75ccbe2b387f42944a490ae92 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
@@ -17,16 +17,28 @@ package nl.lumc.sasc.biopet.core
import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
+/**
+ * Biopet commandline class for java based programs
+ */
trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunctionTrait {
- executable = "java"
+ executable = config("java", default = "java", submodule = "java", freeVar = false)
javaGCThreads = config("java_gc_threads")
javaGCHeapFreeLimit = config("java_gc_heap_freelimit")
javaGCTimeLimit = config("java_gc_timelimit")
- override def javaOpts = super.javaOpts + optional("-Dscala.concurrent.context.numThreads=", threads, spaceSeparated = false, escape = false)
+ /**
+ * Constructs java opts, this adds scala threads
+ * @return
+ */
+ override def javaOpts = super.javaOpts +
+ optional("-Dscala.concurrent.context.numThreads=", threads, spaceSeparated = false, escape = false)
- override def afterGraph {
+ /**
+ * Sets memory limit
+ */
+ override def beforeGraph {
+ super.beforeGraph
memoryLimit = config("memory_limit")
}
@@ -38,7 +50,6 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
preCmdInternal
val cmd = super.commandLine
val finalCmd = executable + cmd.substring(cmd.indexOf(" "))
- // addJobReportBinding("command", cmd)
return cmd
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 1a3f565880dc3a2bd5450efd86cfa188e647eef4..91a9da2a3b79171aba7be7144b8df2fa35675e01 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -23,18 +23,20 @@ import org.broadinstitute.gatk.queue.QSettings
import org.broadinstitute.gatk.queue.function.QFunction
import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
+import scala.collection.mutable.ListBuffer
+/**
+ * Base for biopet pipeline
+ */
trait BiopetQScript extends Configurable with GatkLogging {
@Argument(doc = "JSON config file(s)", fullName = "config_file", shortName = "config", required = false)
val configfiles: List[File] = Nil
- var outputDir: String = {
- val temp = Config.getValueFromMap(Config.global.map, ConfigValueIndex(this.configName, configPath, "output_dir"))
- if (temp.isEmpty) throw new IllegalArgumentException("No output_dir defined in config")
- else {
- val t = temp.get.value.toString
- if (!t.endsWith("/")) t + "/" else t
+ var outputDir: File = {
+ Config.getValueFromMap(globalConfig.map, ConfigValueIndex(this.configName, configPath, "output_dir")) match {
+ case Some(value) => new File(value.asString).getAbsoluteFile
+ case _ => new File(".")
}
}
@@ -43,16 +45,23 @@ trait BiopetQScript extends Configurable with GatkLogging {
var outputFiles: Map[String, File] = Map()
+ /** Get implemented from org.broadinstitute.gatk.queue.QScript */
var qSettings: QSettings
+ /** Get implemented from org.broadinstitute.gatk.queue.QScript */
+ var functions: Seq[QFunction]
+
+ /** Init for pipeline */
def init
- def biopetScript
- var functions: Seq[QFunction]
+ /** Pipeline itself */
+ def biopetScript
+ /**
+ * Script from queue itself, final to force some checks for each pipeline and write report
+ */
final def script() {
- outputDir = config("output_dir", required = true)
- if (!outputDir.endsWith("/")) outputDir += "/"
+ outputDir = config("output_dir").asFile.getAbsoluteFile
init
biopetScript
@@ -61,17 +70,56 @@ trait BiopetQScript extends Configurable with GatkLogging {
case _ =>
}
for (function <- functions) function match {
- case f: BiopetCommandLineFunctionTrait => f.afterGraph
- case _ =>
+ case f: BiopetCommandLineFunctionTrait => {
+ f.preProcesExecutable
+ f.beforeGraph
+ f.commandLine
+ }
+ case _ =>
}
- Config.global.writeReport(qSettings.runName, outputDir + ".log/" + qSettings.runName)
+ if (outputDir.getParentFile.canWrite || (outputDir.exists && outputDir.canWrite))
+ globalConfig.writeReport(qSettings.runName, new File(outputDir, ".log/" + qSettings.runName))
+ else BiopetQScript.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, outputdir can not be created")
+
+ BiopetQScript.checkErrors
}
- def add(functions: QFunction*) // Gets implemeted at org.broadinstitute.sting.queue.QScript
+ /** Get implemented from org.broadinstitute.gatk.queue.QScript */
+ def add(functions: QFunction*)
+
+ /**
+ * Function to set isIntermediate and add in 1 line
+ * @param function
+ * @param isIntermediate
+ */
def add(function: QFunction, isIntermediate: Boolean = false) {
function.isIntermediate = isIntermediate
add(function)
}
+}
+object BiopetQScript extends Logging {
+ private val errors: ListBuffer[Exception] = ListBuffer()
+
+ def addError(error: String, debug: String = null): Unit = {
+ val msg = error + (if (debug != null && logger.isDebugEnabled) "; " + debug else "")
+ errors.append(new Exception(msg))
+ }
+
+ protected def checkErrors: Unit = {
+ if (!errors.isEmpty) {
+ logger.error("*************************")
+ logger.error("Biopet found some errors:")
+ if (logger.isDebugEnabled) {
+ for (e <- errors) {
+ logger.error(e.getMessage)
+ logger.debug(e.getStackTrace.mkString("Stack trace:\n", "\n", "\n"))
+ }
+ } else {
+ errors.map(_.getMessage).sorted.distinct.foreach(logger.error(_))
+ }
+ throw new IllegalStateException("Biopet found errors")
+ }
+ }
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala
index 6fca2dd5d88abae55fc8ecbd0bbc105dbfda6d09..4566cd4f1b26f08f2af84e31735b6514dfd10d6a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala
@@ -17,10 +17,20 @@ package nl.lumc.sasc.biopet.core
import org.apache.log4j.Logger
+/**
+ * Trait to implement logger function on local class/object
+ */
trait Logging {
+ /**
+ *
+ * @return Global biopet logger
+ */
def logger = Logging.logger
}
+/**
+ * Logger object, has a global logger
+ */
object Logging {
val logger = Logger.getRootLogger
}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala
index 369e5267dbc0a162f44b184cc9ee23595122e6ed..cdd226c89f6f2363a452e98116d60b691c1033c1 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala
@@ -15,6 +15,9 @@
*/
package nl.lumc.sasc.biopet.core
+/**
+ * This trait is used in the biopet executable
+ */
trait MainCommand {
lazy val commandName = this.getClass.getSimpleName
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index eb76502c8593a9e970ea2c95b9152569dfffb389..c93cfa7a4c550ea34842e0f1d812eaac332f21d8 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
@@ -28,7 +28,7 @@ trait MultiSampleQScript extends BiopetQScript {
@Argument(doc = "Only Sample", shortName = "sample", required = false)
private val onlySamples: List[String] = Nil
- require(Config.global.map.contains("samples"), "No Samples found in config")
+ require(globalConfig.map.contains("samples"), "No Samples found in config")
/**
* Sample class with basic functions build in
@@ -59,7 +59,7 @@ trait MultiSampleQScript extends BiopetQScript {
def createFile(suffix: String): File = new File(libDir, sampleId + "-" + libId + suffix)
/** Returns library directory */
- def libDir = sampleDir + "lib_" + libId + File.separator
+ def libDir = new File(sampleDir, "lib_" + libId)
/** Function that add library jobs */
protected def addJobs()
@@ -80,7 +80,7 @@ trait MultiSampleQScript extends BiopetQScript {
/** returns a set with library names */
protected def libIds: Set[String] = {
- ConfigUtils.getMapFromPath(Config.global.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
+ ConfigUtils.getMapFromPath(globalConfig.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
}
/** Adds sample jobs */
@@ -108,7 +108,7 @@ trait MultiSampleQScript extends BiopetQScript {
def createFile(suffix: String) = new File(sampleDir, sampleId + suffix)
/** Returns sample directory */
- def sampleDir = outputDir + "samples" + File.separator + sampleId + File.separator
+ def sampleDir = new File(outputDir, "samples" + File.separator + sampleId)
}
/** Sample type, need implementation in pipeline */
@@ -125,7 +125,7 @@ trait MultiSampleQScript extends BiopetQScript {
val samples: Map[String, Sample] = sampleIds.map(id => id -> makeSample(id)).toMap
/** Returns a list of all sampleIDs */
- protected def sampleIds: Set[String] = ConfigUtils.any2map(Config.global.map("samples")).keySet
+ protected def sampleIds: Set[String] = ConfigUtils.any2map(globalConfig.map("samples")).keySet
/** Runs addAndTrackJobs method for each sample */
final def addSamplesJobs() {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
index 60f7112525a92597c8e88c480e87c43bb228105a..8a6d6657ab820aed7fcdff294b8c0f4c768cacb7 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
@@ -20,10 +20,21 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Config
import nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
+/**
+ * Wrapper around executable from Queue
+ */
trait PipelineCommand extends MainCommand with GatkLogging {
+ /**
+ * Gets location of compiled class of pipeline
+ * @return path from classPath to class file
+ */
def pipeline = "/" + getClass.getName.stripSuffix("$").replaceAll("\\.", "/") + ".class"
+ /**
+ * Class can be used directly from java with -cp option
+ * @param args
+ */
def main(args: Array[String]): Unit = {
val argsSize = args.size
for (t <- 0 until argsSize) {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
index b3b25e9a764480f90badc5965fe36f50f22da1fc..53980eadb9e05ef93cc842d822ee75f01c52f67a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
@@ -15,10 +15,16 @@
*/
package nl.lumc.sasc.biopet.core
+/**
+ * Trait for biopet tools, sets some default args
+ */
trait ToolCommand extends MainCommand with Logging {
- protected abstract class AbstractArgs {
- }
+ /** Placeholder for args */
+ protected abstract class AbstractArgs {}
+ /**
+ * Abstract opt parser to add efault args to each biopet tool
+ */
protected abstract class AbstractOptParser extends scopt.OptionParser[Args](commandName) {
opt[String]('l', "log_level") foreach { x =>
x.toLowerCase match {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
index 4ea65cb5a7fc7ceb1226853d47687a0865c818d0..d2fe78ec224c921896e51e04c2f51ad0435e201b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
@@ -43,14 +43,17 @@ class Config(var map: Map[String, Any]) extends Logging {
* @param valueName Name of value
*/
def loadConfigEnv(valueName: String) {
- val globalFiles = sys.env.get(valueName).getOrElse("").split(":")
- if (globalFiles.isEmpty) logger.info(valueName + " value not found, no global config is loaded")
- for (globalFile <- globalFiles) {
- val file: File = new File(globalFile)
- if (file.exists()) {
- logger.info("Loading config file: " + file)
- loadConfigFile(file)
- } else logger.warn(valueName + " value found but file does not exist, no global config is loaded")
+ sys.env.get(valueName) match {
+ case Some(globalFiles) => {
+ for (globalFile <- globalFiles.split(":")) {
+ val file: File = new File(globalFile)
+ if (file.exists) {
+ logger.info("Loading config file: " + file)
+ loadConfigFile(file)
+ } else logger.warn(valueName + " value found but file '" + file + "' does not exist, no global config is loaded")
+ }
+ }
+ case _ => logger.info(valueName + " value not found, no global config is loaded")
}
}
@@ -133,14 +136,15 @@ class Config(var map: Map[String, Any]) extends Logging {
*/
protected[config] def apply(module: String, path: List[String], key: String, default: Any = null, freeVar: Boolean = true): ConfigValue = {
val requestedIndex = ConfigValueIndex(module, path, key, freeVar)
- if (contains(requestedIndex)) return foundCache(requestedIndex)
+ if (contains(requestedIndex)) foundCache(requestedIndex)
else if (default != null) {
defaultCache += (requestedIndex -> ConfigValue(requestedIndex, null, default, freeVar))
- return defaultCache(requestedIndex)
- } else throw new IllegalStateException("Value in config could not be found but it seems required, index: " + requestedIndex)
+ defaultCache(requestedIndex)
+ } else ConfigValue(requestedIndex, null, null, freeVar)
}
- def writeReport(id: String, directory: String): Unit = {
+ def writeReport(id: String, directory: File): Unit = {
+ directory.mkdirs()
def convertIndexValuesToMap(input: List[(ConfigValueIndex, Any)], forceFreeVar: Option[Boolean] = None): Map[String, Any] = {
input.foldLeft(Map[String, Any]())(
@@ -155,8 +159,7 @@ class Config(var map: Map[String, Any]) extends Logging {
}
def writeMapToJsonFile(map: Map[String, Any], name: String): Unit = {
- val file = new File(directory + "/" + id + "." + name + ".json")
- file.getParentFile.mkdirs()
+ val file = new File(directory, id + "." + name + ".json")
val writer = new PrintWriter(file)
writer.write(ConfigUtils.mapToJson(map).spaces2)
writer.close()
@@ -174,7 +177,7 @@ class Config(var map: Map[String, Any]) extends Logging {
val fullEffective = ConfigUtils.mergeMaps(effectiveFound, effectiveDefaultFound)
val fullEffectiveWithNotFound = ConfigUtils.mergeMaps(fullEffective, notFound)
- writeMapToJsonFile(Config.global.map, "input")
+ writeMapToJsonFile(this.map, "input")
writeMapToJsonFile(found, "found")
writeMapToJsonFile(effectiveFound, "effective.found")
writeMapToJsonFile(effectiveDefaultFound, "effective.defaults")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValue.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValue.scala
index c15cd872f8a60fdd39762738a634cc745d2eb50d..bc3b5fc1394a3ae09169a138c39025788552858d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValue.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValue.scala
@@ -25,6 +25,12 @@ class ConfigValue(val requestIndex: ConfigValueIndex, val foundIndex: ConfigValu
*/
def asString = any2string(value)
+ /**
+ * Get value as File
+ * @return value as File
+ */
+ def asFile = new File(any2string(value))
+
/**
* Get value as Int
* @return value as Int
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
index 54e6dfd170a8cb2e68f5c63dd8ca2675513cee7d..df01a54371ee836acdfc93ac41a87d15d7fbce28 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.core.config
import nl.lumc.sasc.biopet.core.Logging
import nl.lumc.sasc.biopet.utils.ConfigUtils.ImplicitConversions
+import scala.collection.JavaConversions._
trait Configurable extends ImplicitConversions {
/** Should be object of parant object */
val root: Configurable
+ def globalConfig: Config = if (root != null) root.globalConfig else Config.global
/** subfix to the path */
def subPath: List[String] = Nil
@@ -79,7 +81,6 @@ trait Configurable extends ImplicitConversions {
* @param key Name of value
* @param default Default value if not found
* @param submodule Adds to the path
- * @param required Default false, if true and value is not found this function will raise an exception
* @param freeVar Default true, if set false value must exist in module
* @param sample Default null, when set path is prefixed with "samples" -> "sampleID"
* @param library Default null, when set path is prefixed with "libraries" -> "libraryID"
@@ -88,7 +89,6 @@ trait Configurable extends ImplicitConversions {
def apply(key: String,
default: Any = null,
submodule: String = null,
- required: Boolean = false,
freeVar: Boolean = true,
sample: String = null,
library: String = null): ConfigValue = {
@@ -100,14 +100,8 @@ trait Configurable extends ImplicitConversions {
val value = Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar))
if (value.isDefined) value.get.value else default
}
- if (!contains(key, submodule, freeVar, sample = s, library = l) && d == null) {
- if (required) {
- Logging.logger.error("Value in config could not be found but it is required, key: " + key + " module: " + m + " path: " + p)
- throw new IllegalStateException("Value in config could not be found but it is required, key: " + key + " module: " + m + " path: " + p)
- } else return null
- }
- if (d == null) return Config.global(m, p, key, freeVar = freeVar)
- else return Config.global(m, p, key, d, freeVar)
+ if (d == null) globalConfig(m, p, key, freeVar = freeVar)
+ else globalConfig(m, p, key, d, freeVar)
}
/**
@@ -129,7 +123,7 @@ trait Configurable extends ImplicitConversions {
val m = if (submodule != null) submodule else configName
val p = path(s, l, submodule)
- Config.global.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
+ globalConfig.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
}
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
index e7467ced6086d1f6cc88d46dc110dc77bafc3809..cbd95512f2bee28b6a85eee03202c5e83ad3ef4e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
@@ -39,14 +39,16 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
+/*
+ * This is a modifed version of org.broadinstitute.gatk.queue.QCommandLine, works without compiling a scala files but used build in class files to skip compile step
+ */
+
package nl.lumc.sasc.biopet.core.workaround
import java.io.File
import org.broadinstitute.gatk.utils.commandline._
import org.broadinstitute.gatk.queue.util._
-import org.broadinstitute.gatk.queue.QCommandPlugin
-import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.queue.QScriptManager
+import org.broadinstitute.gatk.queue.{ QCommandPlugin, QScript, QScriptManager }
import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
import org.broadinstitute.gatk.queue.engine.{ QStatusMessenger, QGraphSettings, QGraph }
import collection.JavaConversions._
@@ -81,19 +83,15 @@ object BiopetQCommandLine extends GatkLogging {
Runtime.getRuntime.addShutdownHook(shutdownHook)
+ CommandLineProgram.start(qCommandLine, argv)
try {
- CommandLineProgram.start(qCommandLine, argv)
- try {
- Runtime.getRuntime.removeShutdownHook(shutdownHook)
- qCommandLine.shutdown()
- } catch {
- case e: Exception => /* ignore, example 'java.lang.IllegalStateException: Shutdown in progress' */
- }
- if (CommandLineProgram.result != 0)
- System.exit(CommandLineProgram.result)
+ Runtime.getRuntime.removeShutdownHook(shutdownHook)
+ qCommandLine.shutdown()
} catch {
- case e: Exception => CommandLineProgram.exitSystemWithError(e)
+ case e: Exception => /* ignore, example 'java.lang.IllegalStateException: Shutdown in progress' */
}
+ if (CommandLineProgram.result != 0)
+ System.exit(CommandLineProgram.result)
}
}
@@ -114,21 +112,28 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
private var qScriptClasses: File = _
private var shuttingDown = false
+ /**
+ * we modified this in Biopet to skip compiling and show full stacktrace again
+ */
private lazy val qScriptPluginManager = {
qScriptClasses = IOUtils.tempDir("Q-Classes-", "", settings.qSettings.tempDirectory)
- //qScriptManager.loadScripts(scripts, qScriptClasses)
- //var temp: Seq[URL] = Seq()
for (t <- scripts) {
val is = getClass.getResourceAsStream(t.getAbsolutePath)
val os = new FileOutputStream(qScriptClasses.getAbsolutePath + "/" + t.getName)
org.apache.commons.io.IOUtils.copy(is, os)
os.close()
- //temp :+= this.getClass.getResource(t.toString)
- //logger.info(this.getClass.getResource(t.toString))
val s = if (t.getName.endsWith("/")) t.getName.substring(0, t.getName.length - 1) else t.getName
pipelineName = s.substring(0, s.lastIndexOf(".")) + "." + System.currentTimeMillis
}
- new PluginManager[QScript](qPluginType, List(qScriptClasses.toURI.toURL))
+
+ // override createByType to pass the correct exceptions
+ new PluginManager[QScript](qPluginType, List(qScriptClasses.toURI.toURL)) {
+ override def createByType(plugintype: Class[_ <: QScript]) = {
+ val noArgsConstructor = plugintype.getDeclaredConstructor()
+ noArgsConstructor.setAccessible(true)
+ noArgsConstructor.newInstance()
+ }
+ }
}
private lazy val qCommandPlugin = {
@@ -186,12 +191,7 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
//if (settings.run)
script.pullInputs()
script.qSettings = settings.qSettings
- try {
- script.script()
- } catch {
- case e: Exception =>
- throw new UserException.CannotExecuteQScript(script.getClass.getSimpleName + ".script() threw the following exception: " + e, e)
- }
+ script.script()
if (remoteFileConverter != null) {
if (remoteFileConverter.convertToRemoteEnabled)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
index e192a845be6db96d2a754d2d2ff6a5e393d136ca..9ac74448e880d7be01063a3f12bdd613141b34a4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
@@ -29,7 +29,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
var R2: File = _
@Input(doc = "The reference file for the bam files.", shortName = "R")
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", shortName = "output")
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
index fed5e514be34618f41d2e8348eba6d15e67fab29..05867d694490ebe64f6d48588f72d4288227e904 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
@@ -48,10 +48,10 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
override def versionCommand = executable + " --version"
override val defaultThreads = 4
- override def afterGraph {
- this.checkExecutable
+ override def beforeGraph {
+ this.preProcesExecutable
- val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
+ val fastqcDir = new File(executable).getParent
contaminants = contaminants match {
// user-defined contaminants file take precedence
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
index 394ad5cdda9d6768d5bd9f72e7019370168f7276..833390259c50e6043e41df55d7200e6ca7e5c2df 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
@@ -30,8 +30,17 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
@Output(doc = "Link destination")
var out: File = _
+ @Output
+ var deps: List[File] = Nil
+
var relative: Boolean = true
+ override def freezeFieldValues(): Unit = {
+ val outLog: String = ".%s.%s.out".format(out.getName, analysisName)
+ jobOutputFile = new File(out.getAbsoluteFile.getParentFile, outLog)
+ super.freezeFieldValues()
+ }
+
lazy val cmd: String = {
lazy val inCanonical: String = {
// need to remove "/~" to correctly expand path with tilde
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
index ea2d704f09ce2388c441338ff25b402606288366..5e5c371bd24ec5019930dcce8ef5bd717c52f08d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
@@ -43,10 +43,10 @@ class Md5sum(val root: Configurable) extends BiopetCommandLineFunction {
}
object Md5sum {
- def apply(root: Configurable, fastqfile: File, outDir: String): Md5sum = {
+ def apply(root: Configurable, fastqfile: File, outDir: File): Md5sum = {
val md5sum = new Md5sum(root)
md5sum.input = fastqfile
- md5sum.output = new File(outDir + fastqfile.getName + ".md5")
+ md5sum.output = new File(outDir, fastqfile.getName + ".md5")
return md5sum
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
index 1d7b45ec9617091a457f073e4110ff5e01932e24..9913254953607dd1542b70ebbf49d2a2dacdd429 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
@@ -64,10 +64,10 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
var executableNonThreads: String = config("exe", default = "raxmlHPC")
var executableThreads: Option[String] = config("exe_pthreads")
- override def afterGraph {
+ override def beforeGraph {
if (threads == 0) threads = getThreads(defaultThreads)
executable = if (threads > 1 && executableThreads.isDefined) executableThreads.get else executableNonThreads
- super.afterGraph
+ super.beforeGraph
out +:= getInfoFile
f match {
case "d" if b.isEmpty => {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
index e732c1023de5f713f4c21ed366da68eddc825285..a041f5dc760543bc0377edc5678299c81ec042c2 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
@@ -47,8 +47,8 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
var verbose: Boolean = config("verbose", default = false)
var noCleanup: Boolean = config("no_cleanup", default = false)
- override def afterGraph: Unit = {
- super.afterGraph
+ override def beforeGraph: Unit = {
+ super.beforeGraph
jobLocalDir = new File(outputDirectory)
if (prefix.isEmpty) prefix = Some(fastafile.getName)
val out: List[String] = List(".recombination_predictions.embl",
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala
index ef5450414b46fcbf793bae9691eaa5f38bb994cd..d30d19fdf36bb1e433b58af626dfd7ad088fd7ec 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala
@@ -51,13 +51,6 @@ class Seqstat(val root: Configurable) extends BiopetCommandLineFunction {
}
object Seqstat {
- def apply(root: Configurable, input: File, output: File): Seqstat = {
- val seqstat = new Seqstat(root)
- seqstat.input = input
- seqstat.output = output
- return seqstat
- }
-
def apply(root: Configurable, fastqfile: File, outDir: String): Seqstat = {
val seqstat = new Seqstat(root)
val ext = fastqfile.getName.substring(fastqfile.getName.lastIndexOf("."))
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
index 5056c70abc0e122fac0b95862f3443faaa48b5c7..abc517962b8302456b333c1f6b6aafe7fdd35a9b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
@@ -53,7 +53,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
override val versionRegex = """sickle version (.*)""".r
override def versionCommand = executable + " --version"
- override def afterGraph {
+ override def beforeGraph {
if (qualityType.isEmpty) qualityType = Some(defaultQualityType)
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
index a7bfeab78447e62eee1634c73ca09c880679327e..bb412a8fbc23a41bf64b905e349b4cc0787c6145 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
@@ -29,13 +29,13 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
var R2: File = _
@Input(doc = "The reference file for the bam files.", shortName = "ref")
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Input(doc = "The genome prefix.")
- var genome: File = config("genome", required = true)
+ var genome: File = config("genome")
@Input(doc = "The hash prefix")
- var hash: File = config("hash", required = true)
+ var hash: File = config("hash")
@Output(doc = "Output file SAM", shortName = "output")
var output: File = _
@@ -54,9 +54,9 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
var sensitive: Boolean = config("sensitive", default = false)
var fast: Boolean = config("fast", default = false)
- var readgroup: String = config("readgroup")
+ var readgroup: String = null
var verbosity: Option[Int] = config("verbosity", default = 2)
- var logfile: String = config("logfile")
+ var logfile: Option[String] = config("logfile")
executable = config("exe", default = "stampy.py", freeVar = false)
override val versionRegex = """stampy v(.*) \(.*\), .*""".r
@@ -68,6 +68,11 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
override def versionCommand = executable + " --help"
+ override def beforeGraph: Unit = {
+ super.beforeGraph
+ require(readgroup != null)
+ }
+
def cmdLine: String = {
var cmd: String = required(executable) +
optional("-t", nCoresRequest) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
index 25fa1876b2abef8a1a6c34555e74d699607f9ba6..9404a895006398d7cd3cca35b3259846af1d6aa0 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
@@ -52,9 +52,9 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", "STAR")
@Argument(doc = "Output Directory")
- var outputDir: String = _
+ var outputDir: File = _
- var genomeDir: String = config("genomeDir", reference.getParent + "/star/")
+ var genomeDir: File = config("genomeDir", new File(reference.getAbsoluteFile.getParent, "star"))
var runmode: String = _
var sjdbOverhang: Int = _
var outFileNamePrefix: String = _
@@ -62,9 +62,8 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
override val defaultVmem = "6G"
override val defaultThreads = 8
- override def afterGraph() {
+ override def beforeGraph() {
if (outFileNamePrefix != null && !outFileNamePrefix.endsWith(".")) outFileNamePrefix += "."
- if (!outputDir.endsWith("/")) outputDir += "/"
val prefix = if (outFileNamePrefix != null) outputDir + outFileNamePrefix else outputDir
if (runmode == null) {
outputSam = new File(prefix + "Aligned.out.sam")
@@ -97,36 +96,35 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
}
object Star {
- def apply(configurable: Configurable, R1: File, R2: File, outputDir: String, isIntermediate: Boolean = false, deps: List[File] = Nil): Star = {
+ def apply(configurable: Configurable, R1: File, R2: File, outputDir: File, isIntermediate: Boolean = false, deps: List[File] = Nil): Star = {
val star = new Star(configurable)
star.R1 = R1
if (R2 != null) star.R2 = R2
star.outputDir = outputDir
star.isIntermediate = isIntermediate
star.deps = deps
- star.afterGraph
+ star.beforeGraph
return star
}
- def _2pass(configurable: Configurable, R1: File, R2: File, outputDir: String, isIntermediate: Boolean = false, deps: List[File] = Nil): (File, List[Star]) = {
- val outDir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
- val starCommand_pass1 = Star(configurable, R1, if (R2 != null) R2 else null, outDir + "aln-pass1/")
+ def _2pass(configurable: Configurable, R1: File, R2: File, outputDir: File, isIntermediate: Boolean = false, deps: List[File] = Nil): (File, List[Star]) = {
+ val starCommand_pass1 = Star(configurable, R1, if (R2 != null) R2 else null, new File(outputDir, "aln-pass1"))
starCommand_pass1.isIntermediate = isIntermediate
starCommand_pass1.deps = deps
- starCommand_pass1.afterGraph
+ starCommand_pass1.beforeGraph
val starCommand_reindex = new Star(configurable)
starCommand_reindex.sjdbFileChrStartEnd = starCommand_pass1.outputTab
- starCommand_reindex.outputDir = outDir + "re-index/"
+ starCommand_reindex.outputDir = new File(outputDir, "re-index")
starCommand_reindex.runmode = "genomeGenerate"
starCommand_reindex.isIntermediate = isIntermediate
- starCommand_reindex.afterGraph
+ starCommand_reindex.beforeGraph
- val starCommand_pass2 = Star(configurable, R1, if (R2 != null) R2 else null, outDir + "aln-pass2/")
+ val starCommand_pass2 = Star(configurable, R1, if (R2 != null) R2 else null, new File(outputDir, "aln-pass2"))
starCommand_pass2.genomeDir = starCommand_reindex.outputDir
starCommand_pass2.isIntermediate = isIntermediate
starCommand_pass2.deps = deps
- starCommand_pass2.afterGraph
+ starCommand_pass2.beforeGraph
return (starCommand_pass2.outputSam, List(starCommand_pass1, starCommand_reindex, starCommand_pass2))
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
index e0b8bd68bda46a6b3dc6915a54482b093cfd43d6..ce86a1ed9bd1e8d1afa04867887be2f21cf6231b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
@@ -29,7 +29,7 @@ class TopHat(val root: Configurable) extends BiopetCommandLineFunction {
var R2: File = _
@Input(doc = "Bowtie index", shortName = "bti")
- var bowtie_index: File = config("bowtie_index", required = true)
+ var bowtie_index: File = config("bowtie_index")
@Argument(doc = "Output Directory")
var outputDir: String = _
@@ -64,7 +64,7 @@ class TopHat(val root: Configurable) extends BiopetCommandLineFunction {
override def versionCommand = executable + " --version"
- override def afterGraph() {
+ override def beforeGraph() {
if (!outputDir.endsWith("/")) outputDir += "/"
output = new File(outputDir + "accepted_hits.bam")
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
index 531425b7a50bde7a77d62213561cef91095ecdd9..9c98893c9a4f22216cbcc57041bf7ca65b50be7e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
@@ -14,10 +14,10 @@ class WigToBigWig(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Input wig file")
var inputWigFile: File = _
- @Input(doc = "Input chrom sizes file")
+ @Input(doc = "Input chrom sizes file", required = true)
var inputChromSizesFile: File = _
- @Output(doc = "Output BigWig file")
+ @Output(doc = "Output BigWig file", required = true)
var outputBigWig: File = _
executable = config("exe", default = "wigToBigWig")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
index bfd0a5846e6531b47f285453a2d848b1b7f1bafe..3298702fcfd5cd98e1eaf0bae8f6b059d353d2c9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
@@ -13,7 +13,7 @@ class BwaAln(val root: Configurable) extends Bwa {
var fastq: File = _
@Input(doc = "The reference file for the bam files.", required = true)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", required = false)
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
index fc790b183b5bae2922a1b5f89ec66fcf4f5b85b2..74cdad0cea290e5a8cdcc2b360fa3fa32444791c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
@@ -29,7 +29,7 @@ class BwaMem(val root: Configurable) extends Bwa {
var R2: File = _
@Input(doc = "The reference file for the bam files.", shortName = "R")
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", shortName = "output")
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
index b857eea014ac52acb9608debb94db9cd75cef929..255811561e732b229b1417c95d866fad4694c0c9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
@@ -26,7 +26,7 @@ class BwaSampe(val root: Configurable) extends Bwa {
var saiR2: File = _
@Input(doc = "The reference file for the bam files.", required = true)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", required = false)
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
index 51f9a0f30eaf73a897fefaa2b6cf69d4e3386b62..8bbf918474e21d2e2837ce01d5bc4490e13bd087 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
@@ -16,7 +16,7 @@ class BwaSamse(val root: Configurable) extends Bwa {
var sai: File = _
@Input(doc = "The reference file for the bam files.", required = true)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", required = false)
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
index 02c0f09584206770965e67e6afc32765f9997a3f..fc1e0a8628e3c03c3b88a06c032317bcc43eedd1 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
@@ -28,8 +28,8 @@ class ConiferExport(val root: Configurable) extends Conifer {
@Output(doc = "Output <sample>.svdzrpkm.bed", shortName = "out", required = true)
var output: File = _
- override def afterGraph {
- this.checkExecutable
+ override def beforeGraph {
+ this.preProcesExecutable
}
override def cmdLine = super.cmdLine +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
index d017864f6988828100f6bbda421fbf734a9a5878..aff6ee16cdfbf1a77529d079bc1789c9ffcc494b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
@@ -9,6 +9,6 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
abstract class IGVTools extends BiopetCommandLineFunction {
executable = config("exe", default = "igvtools", submodule = "igvtools", freeVar = false)
override def versionCommand = executable + " version"
- override val versionRegex = """IGV Version: ([\d\.]) .*""".r
+ override val versionRegex = """IGV Version:? ([\w\.]*) .*""".r
override val versionExitcode = List(0)
}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
index 8037616834ecd4de02e9949883b75d20b45c7347..b62c852f9f40578131d734d206531e77236fb595 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
@@ -1,8 +1,6 @@
package nl.lumc.sasc.biopet.extensions.igvtools
-import java.nio.file.InvalidPathException
-
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import java.io.{ FileNotFoundException, File }
@@ -13,19 +11,18 @@ import java.io.{ FileNotFoundException, File }
* @constructor create a new IGVTools instance from a `.bam` file
*
*/
-
class IGVToolsCount(val root: Configurable) extends IGVTools {
@Input(doc = "Bam File")
var input: File = _
- @Input(doc = "<genome>.chrom.sizes File")
+ @Input(doc = "<genome>.chrom.sizes File", required = true)
var genomeChromSizes: File = _
@Output
- var tdf: Option[File] = _
+ var tdf: Option[File] = None
@Output
- var wig: Option[File] = _
+ var wig: Option[File] = None
var maxZoom: Option[Int] = config("maxZoom")
var windowSize: Option[Int] = config("windowSize")
@@ -44,12 +41,13 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
var pairs: Boolean = config("pairs", default = false)
- override def afterGraph {
- super.afterGraph
- if (!input.exists()) throw new FileNotFoundException("Input bam is required for IGVToolsCount")
+ override def beforeGraph {
+ super.beforeGraph
- if (!wig.isEmpty && !wig.get.getAbsolutePath.endsWith(".wig")) throw new IllegalArgumentException("Wiggle file should have a .wig file-extension")
- if (!tdf.isEmpty && !tdf.get.getAbsolutePath.endsWith(".tdf")) throw new IllegalArgumentException("TDF file should have a .tdf file-extension")
+ wig.foreach(x => if (!x.getAbsolutePath.endsWith(".wig"))
+ throw new IllegalArgumentException("WIG file should have a .wig file-extension"))
+ tdf.foreach(x => if (!x.getAbsolutePath.endsWith(".tdf"))
+ throw new IllegalArgumentException("TDF file should have a .tdf file-extension"))
}
def cmdLine = {
@@ -102,4 +100,4 @@ object IGVToolsCount {
counting.genomeChromSizes = genomeChromSizes
return counting
}
-}
\ No newline at end of file
+}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
index e6a9c48e925949bdd413a9aca79afbb7e28b91d7..8224fd4713f00d47511156459b02f5b733e1deda 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
@@ -55,7 +55,7 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
var broadcutoff: Option[Int] = config("broadcutoff")
var callsummits: Boolean = config("callsummits", default = false)
- override def afterGraph: Unit = {
+ override def beforeGraph: Unit = {
if (name.isEmpty) throw new IllegalArgumentException("Name is not defined")
if (outputdir == null) throw new IllegalArgumentException("Outputdir is not defined")
output_narrow = new File(outputdir + name.get + ".narrowPeak")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
index a48cd8cfe611e854202f137b2b1dbe5ee2cd295f..4aa970f636ddbbb7216abce5d96ebbbebc8a7598 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
@@ -58,7 +58,7 @@ class CalculateHsMetrics(val root: Configurable) extends Picard {
}
object CalculateHsMetrics {
- def apply(root: Configurable, input: File, baitIntervals: File, targetIntervals: File, outputDir: String): CalculateHsMetrics = {
+ def apply(root: Configurable, input: File, baitIntervals: File, targetIntervals: File, outputDir: File): CalculateHsMetrics = {
val calculateHsMetrics = new CalculateHsMetrics(root)
calculateHsMetrics.input = input
calculateHsMetrics.baitIntervals = baitIntervals
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
index b2553c47e2bf05bc14dd87f667cf80d0165181ce..6606d9e41acc4d5c2b785f905d844c2f91676b72 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
@@ -62,7 +62,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard {
}
object CollectAlignmentSummaryMetrics {
- def apply(root: Configurable, input: File, outputDir: String): CollectAlignmentSummaryMetrics = {
+ def apply(root: Configurable, input: File, outputDir: File): CollectAlignmentSummaryMetrics = {
val collectAlignmentSummaryMetrics = new CollectAlignmentSummaryMetrics(root)
collectAlignmentSummaryMetrics.input = input
collectAlignmentSummaryMetrics.output = new File(outputDir, input.getName.stripSuffix(".bam") + ".alignmentMetrics")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
index 7ffcb50d8fec02138c07e4fc95d7608e8bfba72e..86198d2a344489a62b546f5d9c0dd4a8234c929a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
@@ -35,7 +35,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard {
var outputSummary: File = _
@Argument(doc = "Reference file", required = false)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Argument(doc = "Window size", required = false)
var windowSize: Option[Int] = config("windowsize")
@@ -49,7 +49,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard {
@Argument(doc = "IS_BISULFITE_SEQUENCED", required = false)
var isBisulfiteSequinced: Option[Boolean] = config("isbisulfitesequinced")
- override def afterGraph {
+ override def beforeGraph {
if (outputChart == null) outputChart = new File(output + ".pdf")
//require(reference.exists)
}
@@ -67,7 +67,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard {
}
object CollectGcBiasMetrics {
- def apply(root: Configurable, input: File, outputDir: String): CollectGcBiasMetrics = {
+ def apply(root: Configurable, input: File, outputDir: File): CollectGcBiasMetrics = {
val collectGcBiasMetrics = new CollectGcBiasMetrics(root)
collectGcBiasMetrics.input :+= input
collectGcBiasMetrics.output = new File(outputDir, input.getName.stripSuffix(".bam") + ".gcbiasmetrics")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
index 7d7c7ddc2e773601e772ea3e1fc744f97059f5cb..9b1777677a9567d8e88d21f44ec7f913e45341b5 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
@@ -54,7 +54,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard {
@Argument(doc = "HISTOGRAM_WIDTH", required = false)
var histogramWidth: Option[Int] = config("histogramWidth")
- override def afterGraph {
+ override def beforeGraph {
if (outputHistogram == null) outputHistogram = new File(output + ".pdf")
//require(reference.exists)
}
@@ -72,7 +72,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard {
}
object CollectInsertSizeMetrics {
- def apply(root: Configurable, input: File, outputDir: String): CollectInsertSizeMetrics = {
+ def apply(root: Configurable, input: File, outputDir: File): CollectInsertSizeMetrics = {
val collectInsertSizeMetrics = new CollectInsertSizeMetrics(root)
collectInsertSizeMetrics.input = input
collectInsertSizeMetrics.output = new File(outputDir, input.getName.stripSuffix(".bam") + ".insertsizemetrics")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
index 6df04c12ccb0ad1ca1c4853dac940ec3a304d043..181494ae12235f2fc95bade2098a9d313f6309b8 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
@@ -70,8 +70,8 @@ class MarkDuplicates(val root: Configurable) extends Picard {
@Output(doc = "Bam Index", required = true)
private var outputIndex: File = _
- override def afterGraph {
- super.afterGraph
+ override def beforeGraph {
+ super.beforeGraph
if (createIndex) outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
index 4de143498d9812502a2141facfacc0bbf2b046d5..8feaf782ac57aba5a6779e515fe2c6ce452f5871 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
@@ -53,7 +53,7 @@ class MergeSamFiles(val root: Configurable) extends Picard {
}
object MergeSamFiles {
- def apply(root: Configurable, input: List[File], outputDir: String, sortOrder: String = null): MergeSamFiles = {
+ def apply(root: Configurable, input: List[File], outputDir: File, sortOrder: String = null): MergeSamFiles = {
val mergeSamFiles = new MergeSamFiles(root)
mergeSamFiles.input = input
mergeSamFiles.output = new File(outputDir, input.head.getName.stripSuffix(".bam").stripSuffix(".sam") + ".merge.bam")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
index 56cfec1dd668c5a4c3bb349276e0fcf25729a040..ef7ec250d5de2bd88c36e48af157ae29bce0a3b0 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
@@ -34,8 +34,8 @@ class SortSam(val root: Configurable) extends Picard {
@Output(doc = "Bam Index", required = true)
private var outputIndex: File = _
- override def afterGraph {
- super.afterGraph
+ override def beforeGraph {
+ super.beforeGraph
if (createIndex) outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
index b57e6773299720ddc7fbb7deb7933d4d10721795..a4833d5f17c509fc0a47ca77a631e2ec32596bd1 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
@@ -30,22 +30,10 @@ class SamtoolsFlagstat(val root: Configurable) extends Samtools {
}
object SamtoolsFlagstat {
- def apply(root: Configurable, input: File, output: File): SamtoolsFlagstat = {
+ def apply(root: Configurable, input: File, outputDir: File): SamtoolsFlagstat = {
val flagstat = new SamtoolsFlagstat(root)
flagstat.input = input
- flagstat.output = output
- return flagstat
+ flagstat.output = new File(outputDir, input.getName.stripSuffix(".bam") + ".flagstat")
+ flagstat
}
-
- def apply(root: Configurable, input: File, outputDir: String): SamtoolsFlagstat = {
- val dir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
- val outputFile = new File(dir + swapExtension(input.getName))
- return apply(root, input, outputFile)
- }
-
- def apply(root: Configurable, input: File): SamtoolsFlagstat = {
- return apply(root, input, new File(swapExtension(input.getAbsolutePath)))
- }
-
- private def swapExtension(inputFile: String) = inputFile.stripSuffix(".bam") + ".flagstat"
}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/SquishBed.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/SquishBed.scala
index d349b8d1d944a96332e5a01b686271dfd88e36ca..0a86da49ddd2f0c8eb20d6707b6c25e3d33d0c89 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/SquishBed.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/SquishBed.scala
@@ -35,7 +35,7 @@ class SquishBed(val root: Configurable) extends PythonCommandLineFunction {
}
object SquishBed {
- def apply(root: Configurable, input: File, outputDir: String): SquishBed = {
+ def apply(root: Configurable, input: File, outputDir: File): SquishBed = {
val squishBed = new SquishBed(root)
squishBed.input = input
squishBed.output = new File(outputDir, input.getName.stripSuffix(".bed") + ".squish.bed")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
index 3aa5a2282facaf9e59b483713222369b015488f0..6f4ffbcd2c72997767edb9a5902d1eb1846552f6 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
@@ -40,17 +40,11 @@ class BiopetFlagstat(val root: Configurable) extends BiopetJavaCommandLineFuncti
}
object BiopetFlagstat extends ToolCommand {
- def apply(root: Configurable, input: File, output: File): BiopetFlagstat = {
- val flagstat = new BiopetFlagstat(root)
- flagstat.input = input
- flagstat.output = output
- return flagstat
- }
- def apply(root: Configurable, input: File, outputDir: String): BiopetFlagstat = {
+ def apply(root: Configurable, input: File, outputDir: File): BiopetFlagstat = {
val flagstat = new BiopetFlagstat(root)
flagstat.input = input
flagstat.output = new File(outputDir, input.getName.stripSuffix(".bam") + ".biopetflagstat")
- return flagstat
+ flagstat
}
case class Args(inputFile: File = null, region: Option[String] = None) extends AbstractArgs
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
index aaa2797b65930d197089aaa72d90dd5e4d9382e4..2c930f3bec310806e915bd90fdce71a58efb6a13 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
@@ -34,22 +34,24 @@ class FastqSync(val root: Configurable) extends BiopetJavaCommandLineFunction {
javaMainClass = getClass.getName
@Input(doc = "Original FASTQ file (read 1 or 2)", shortName = "r", required = true)
- var refFastq: File = _
+ var refFastq: File = null
@Input(doc = "Input read 1 FASTQ file", shortName = "i", required = true)
- var inputFastq1: File = _
+ var inputFastq1: File = null
@Input(doc = "Input read 2 FASTQ file", shortName = "j", required = true)
- var inputFastq2: File = _
+ var inputFastq2: File = null
@Output(doc = "Output read 1 FASTQ file", shortName = "o", required = true)
- var outputFastq1: File = _
+ var outputFastq1: File = null
@Output(doc = "Output read 2 FASTQ file", shortName = "p", required = true)
- var outputFastq2: File = _
+ var outputFastq2: File = null
@Output(doc = "Sync statistics", required = true)
- var outputStats: File = _
+ var outputStats: File = null
+
+ override val defaultVmem = "5G"
// executed command line
override def commandLine =
@@ -90,25 +92,14 @@ class FastqSync(val root: Configurable) extends BiopetJavaCommandLineFunction {
object FastqSync extends ToolCommand {
- /**
- * Implicit class to allow for lazy retrieval of FastqRecord ID
- * without any read pair mark
- *
- * @param fq FastqRecord
- */
+ /** Regex for capturing read ID ~ taking into account its read pair mark (if present) */
+ private val idRegex = "[_/][12]\\s??|\\s".r
+
+ /** Implicit class to allow for lazy retrieval of FastqRecord ID without any read pair mark */
private implicit class FastqPair(fq: FastqRecord) {
- lazy val fragId = fq.getReadHeader.split("[_/][12]\\s??|\\s")(0)
+ lazy val fragId = idRegex.split(fq.getReadHeader)(0)
}
- /**
- * Counts from syncing FastqRecords
- *
- * @param numDiscard1 Number of reads discarded from the initial read 1
- * @param numDiscard2 Number of reads discarded from the initial read 2
- * @param numKept Number of items in result
- */
- case class SyncCounts(numDiscard1: Int, numDiscard2: Int, numKept: Int)
-
/**
* Filters out FastqRecord that are not present in the input iterators, using
* a reference sequence object
@@ -118,7 +109,8 @@ object FastqSync extends ToolCommand {
* @param seqB FastqReader over read 2
* @return
*/
- def syncFastq(pre: FastqReader, seqA: FastqReader, seqB: FastqReader): (Stream[(FastqRecord, FastqRecord)], SyncCounts) = {
+ def syncFastq(pre: FastqReader, seqA: FastqReader, seqB: FastqReader,
+ seqOutA: AsyncFastqWriter, seqOutB: AsyncFastqWriter): (Long, Long, Long) = {
// counters for discarded A and B seqections + total kept
// NOTE: we are reasigning values to these variables in the recursion below
var (numDiscA, numDiscB, numKept) = (0, 0, 0)
@@ -129,72 +121,50 @@ object FastqSync extends ToolCommand {
* @param pre Reference sequence, assumed to be a superset of both seqA and seqB
* @param seqA Sequence over read 1
* @param seqB Sequence over read 2
- * @param acc Stream containing pairs which are present in read 1 and read 2
* @return
*/
@tailrec def syncIter(pre: Stream[FastqRecord],
- seqA: Stream[FastqRecord], seqB: Stream[FastqRecord],
- acc: Stream[(FastqRecord, FastqRecord)]): Stream[(FastqRecord, FastqRecord)] =
+ seqA: Stream[FastqRecord], seqB: Stream[FastqRecord]): Unit =
(pre.headOption, seqA.headOption, seqB.headOption) match {
+ // where the magic happens!
+ case (Some(r), Some(a), Some(b)) =>
+ val (nextA, nextB) = (a.fragId == r.fragId, b.fragId == r.fragId) match {
+ // all IDs are equal to ref
+ case (true, true) =>
+ numKept += 1
+ seqOutA.write(a)
+ seqOutB.write(b)
+ (seqA.tail, seqB.tail)
+ // B not equal to ref and A is equal, then we discard A and progress
+ case (true, false) =>
+ numDiscA += 1
+ (seqA.tail, seqB)
+ // A not equal to ref and B is equal, then we discard B and progress
+ case (false, true) =>
+ numDiscB += 1
+ (seqA, seqB.tail)
+ case (false, false) =>
+ (seqA, seqB)
+ }
+ syncIter(pre.tail, nextA, nextB)
// recursion base case: both iterators have been exhausted
- case (_, None, None) => acc
+ case (_, None, None) => ;
// illegal state: reference sequence exhausted but not seqA or seqB
case (None, Some(_), _) | (None, _, Some(_)) =>
throw new NoSuchElementException("Reference record stream shorter than expected")
// keep recursion going if A still has items (we want to count how many)
case (_, _, None) =>
numDiscA += 1
- syncIter(pre.tail, seqA.tail, Stream(), acc)
+ syncIter(pre.tail, seqA.tail, seqB)
// like above but for B
case (_, None, _) =>
numDiscB += 1
- syncIter(pre.tail, Stream(), seqB.tail, acc)
- // where the magic happens!
- case (Some(r), Some(a), Some(b)) =>
- // value of A iterator in the next recursion
- val nextA =
- // hold A if its head is not equal to reference
- if (a.fragId != r.fragId) {
- if (b.fragId == r.fragId) numDiscB += 1
- seqA
- // otherwise, go to next item
- } else seqA.tail
- // like A above
- val nextB =
- if (b.fragId != r.fragId) {
- if (a.fragId == r.fragId) numDiscA += 1
- seqB
- } else seqB.tail
- // value of accumulator in the next recursion
- val nextAcc =
- // keep accumulator unchanged if any of the two post streams
- // have different elements compared to the reference stream
- if (a.fragId != r.fragId || b.fragId != r.fragId) acc
- // otherwise, grow accumulator
- else {
- numKept += 1
- acc ++ Stream((a, b))
- }
- syncIter(pre.tail, nextA, nextB, nextAcc)
+ syncIter(pre.tail, seqA, seqB.tail)
}
- (syncIter(pre.iterator.asScala.toStream, seqA.iterator.asScala.toStream, seqB.iterator.asScala.toStream,
- Stream.empty[(FastqRecord, FastqRecord)]),
- SyncCounts(numDiscA, numDiscB, numKept))
- }
+ syncIter(pre.iterator.asScala.toStream, seqA.iterator.asScala.toStream, seqB.iterator.asScala.toStream)
- def writeSyncedFastq(sync: Stream[(FastqRecord, FastqRecord)],
- counts: SyncCounts,
- outputFastq1: AsyncFastqWriter,
- outputFastq2: AsyncFastqWriter): Unit = {
- sync.foreach {
- case (rec1, rec2) =>
- outputFastq1.write(rec1)
- outputFastq2.write(rec2)
- }
- println("Filtered %d reads from first read file.".format(counts.numDiscard1))
- println("Filtered %d reads from second read file.".format(counts.numDiscard2))
- println("Synced read files contain %d reads.".format(counts.numKept))
+ (numDiscA, numDiscB, numKept)
}
/** Function to merge this tool's summary with summaries from other objects */
@@ -229,7 +199,6 @@ object FastqSync extends ToolCommand {
class OptParser extends AbstractOptParser {
- // TODO: make output format independent from input format?
head(
s"""
|$commandName - Sync paired-end FASTQ files.
@@ -279,15 +248,23 @@ object FastqSync extends ToolCommand {
val commandArgs: Args = parseArgs(args)
- val (synced, counts) = syncFastq(
- new FastqReader(commandArgs.refFastq),
- new FastqReader(commandArgs.inputFastq1),
- new FastqReader(commandArgs.inputFastq2))
-
- writeSyncedFastq(synced, counts,
- // using 3000 for queue size to approximate NFS buffer
- new AsyncFastqWriter(new BasicFastqWriter(commandArgs.outputFastq1), 3000),
- new AsyncFastqWriter(new BasicFastqWriter(commandArgs.outputFastq2), 3000)
- )
+ val refReader = new FastqReader(commandArgs.refFastq)
+ val AReader = new FastqReader(commandArgs.inputFastq1)
+ val BReader = new FastqReader(commandArgs.inputFastq2)
+ val AWriter = new AsyncFastqWriter(new BasicFastqWriter(commandArgs.outputFastq1), 3000)
+ val BWriter = new AsyncFastqWriter(new BasicFastqWriter(commandArgs.outputFastq2), 3000)
+
+ try {
+ val (numDiscA, numDiscB, numKept) = syncFastq(refReader, AReader, BReader, AWriter, BWriter)
+ println(s"Filtered $numDiscA reads from first read file.")
+ println(s"Filtered $numDiscB reads from second read file.")
+ println(s"Synced files contain $numKept reads.")
+ } finally {
+ refReader.close()
+ AReader.close()
+ BReader.close()
+ AWriter.close()
+ BWriter.close()
+ }
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
index c431aa0dac3a5a5a39c8ab676a704ac3645a4ad9..3eec803c8dab66d824a86a71f794d691ebde2ba6 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
@@ -49,8 +49,8 @@ class MergeAlleles(val root: Configurable) extends BiopetJavaCommandLineFunction
override val defaultVmem = "8G"
memoryLimit = Option(4)
- override def afterGraph {
- super.afterGraph
+ override def beforeGraph {
+ super.beforeGraph
if (output.getName.endsWith(".gz")) outputIndex = new File(output.getAbsolutePath + ".tbi")
if (output.getName.endsWith(".vcf")) outputIndex = new File(output.getAbsolutePath + ".idx")
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
index ae21c34e4b820ebfb0b33e3b033196e03a58ef6e..3e9743fb16e7c1d9228307a22ca950ee8f18eb0d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
@@ -54,8 +54,8 @@ class MpileupToVcf(val root: Configurable) extends BiopetJavaCommandLineFunction
override def defaults = ConfigUtils.mergeMaps(Map("samtoolsmpileup" -> Map("disable_baq" -> true, "min_map_quality" -> 1)),
super.defaults)
- override def afterGraph {
- super.afterGraph
+ override def beforeGraph {
+ super.beforeGraph
val samtoolsMpileup = new SamtoolsMpileup(this)
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
index 11d930d5972897824e341d22d46808d849d7767b..81a0b83c3c3555aa7108d65821cafb94371e186c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
@@ -21,15 +21,15 @@ class VcfStats(val root: Configurable) extends BiopetJavaCommandLineFunction {
@Input(doc = "Input fastq", shortName = "I", required = true)
var input: File = _
- protected var outputDir: String = _
+ protected var outputDir: File = _
/**
* Set output dir and a output file
* @param dir
*/
- def setOutputDir(dir: String): Unit = {
+ def setOutputDir(dir: File): Unit = {
outputDir = dir
- this.jobOutputFile = new File(dir + File.separator + ".vcfstats.out")
+ this.jobOutputFile = new File(dir, ".vcfstats.out")
}
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
index 9f1cddb7913cf7846daa72c7b9e695988b3a14c6..2c9ae7e6a87b977001ff94668db1d768511b378f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
@@ -16,6 +16,7 @@
package nl.lumc.sasc.biopet.utils
import java.io.File
+import nl.lumc.sasc.biopet.core.BiopetQScript
import nl.lumc.sasc.biopet.core.Logging
import nl.lumc.sasc.biopet.core.config.ConfigValue
import argonaut._, Argonaut._
@@ -32,7 +33,8 @@ object ConfigUtils extends Logging {
* @param map2 Backup for map1
* @return merged map
*/
- def mergeMaps(map1: Map[String, Any], map2: Map[String, Any]): Map[String, Any] = {
+ def mergeMaps(map1: Map[String, Any], map2: Map[String, Any],
+ resolveConflict: (Any, Any, String) => Any = (m1, m2, key) => m1): Map[String, Any] = {
var newMap: Map[String, Any] = Map()
for (key <- map1.keySet.++(map2.keySet)) {
if (!map2.contains(key)) newMap += (key -> map1(key))
@@ -45,7 +47,7 @@ object ConfigUtils extends Logging {
case _ => newMap += (key -> map1(key))
}
}
- case _ => newMap += (key -> map1(key))
+ case _ => newMap += (key -> resolveConflict(map1(key), map2(key), key))
}
}
}
@@ -330,14 +332,27 @@ object ConfigUtils extends Logging {
trait ImplicitConversions {
import scala.language.implicitConversions
+ private def requiredValue(value: ConfigValue): Boolean = {
+ val exist = valueExists(value)
+ if (!exist)
+ BiopetQScript.addError("Value does not exist but is required, key: " + value.requestIndex.key +
+ " module: " + value.requestIndex.module,
+ (if (value.requestIndex.path != Nil) " path: " + value.requestIndex.path.mkString("->") else null))
+ exist
+ }
+
+ private def valueExists(value: ConfigValue): Boolean = {
+ value != null && value.value != null && value.value != None
+ }
+
/**
* Convert ConfigValue to File
* @param value Input ConfigValue
* @return
*/
implicit def configValue2file(value: ConfigValue): File = {
- if (value != null && value.value != null && value.value != None) new File(any2string(value.value))
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) new File(any2string(value.value))
+ else new File("")
}
/**
@@ -346,7 +361,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionFile(value: ConfigValue): Option[File] = {
- if (value != null && value.value != null && value.value != None) Some(new File(any2string(value.value)))
+ if (valueExists(value)) Some(new File(any2string(value.value)))
else None
}
@@ -356,8 +371,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2string(value: ConfigValue): String = {
- if (value != null && value.value != null && value.value != None) any2string(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2string(value.value)
+ else ""
}
/**
@@ -366,7 +381,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionString(value: ConfigValue): Option[String] = {
- if (value != null && value.value != null && value.value != None) Some(any2string(value.value))
+ if (valueExists(value)) Some(any2string(value.value))
else None
}
@@ -376,8 +391,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2long(value: ConfigValue): Long = {
- if (value != null && value.value != null && value.value != None) any2long(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2long(value.value)
+ else 0L
}
/**
@@ -386,7 +401,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionLong(value: ConfigValue): Option[Long] = {
- if (value != null && value.value != null && value.value != None) Option(any2long(value.value))
+ if (valueExists(value)) Option(any2long(value.value))
else None
}
@@ -396,8 +411,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2int(value: ConfigValue): Int = {
- if (value != null && value.value != null && value.value != None) any2int(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2int(value.value)
+ else 0
}
/**
@@ -406,7 +421,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionInt(value: ConfigValue): Option[Int] = {
- if (value != null && value.value != null && value.value != None) Option(any2int(value.value))
+ if (valueExists(value)) Option(any2int(value.value))
else None
}
@@ -416,8 +431,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2double(value: ConfigValue): Double = {
- if (value != null && value.value != null && value.value != None) any2double(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2double(value.value)
+ else 0.0
}
/**
@@ -426,7 +441,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionDouble(value: ConfigValue): Option[Double] = {
- if (value != null && value.value != null && value.value != None) Option(any2double(value.value))
+ if (valueExists(value)) Option(any2double(value.value))
else None
}
@@ -436,8 +451,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2float(value: ConfigValue): Float = {
- if (value != null && value.value != null && value.value != None) any2float(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2float(value.value)
+ else 0f
}
/**
@@ -446,7 +461,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionFloat(value: ConfigValue): Option[Float] = {
- if (value != null && value.value != null && value.value != None) Option(any2float(value.value))
+ if (valueExists(value)) Option(any2float(value.value))
else None
}
@@ -456,8 +471,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2boolean(value: ConfigValue): Boolean = {
- if (value != null && value.value != null && value.value != None) any2boolean(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2boolean(value.value)
+ else false
}
/**
@@ -466,7 +481,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionBoolean(value: ConfigValue): Option[Boolean] = {
- if (value != null && value.value != null && value.value != None) Option(any2boolean(value.value))
+ if (valueExists(value)) Option(any2boolean(value.value))
else None
}
@@ -476,8 +491,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2list(value: ConfigValue): List[Any] = {
- if (value != null && value.value != null && value.value != None) any2list(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2list(value.value)
+ else Nil
}
/**
@@ -486,8 +501,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2stringList(value: ConfigValue): List[String] = {
- if (value != null && value.value != null && value.value != None) any2stringList(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2stringList(value.value)
+ else Nil
}
/**
@@ -496,8 +511,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2stringSet(value: ConfigValue): Set[String] = {
- if (value != null && value.value != null && value.value != None) any2stringList(value.value).toSet
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2stringList(value.value).toSet
+ else Set()
}
/**
@@ -506,8 +521,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2map(value: ConfigValue): Map[String, Any] = {
- if (value != null && value.value != null && value.value != None) any2map(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2map(value.value)
+ else Map()
}
}
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
index 92d0b9f63f60ad1a6c9489ba1d71fd3f25ab6828..0adc3a09b554ea489c9e0c10e0f25d7d785a3bdd 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
@@ -1,9 +1,7 @@
package nl.lumc.sasc.biopet.core.config
-import nl.lumc.sasc.biopet.utils.ConfigUtils._
import nl.lumc.sasc.biopet.utils.{ ConfigUtilsTest, ConfigUtils }
import org.scalatest.Matchers
-import org.scalatest.mock.MockitoSugar
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{ DataProvider, Test }
@@ -30,9 +28,6 @@ class ConfigTest extends TestNGSuite with Matchers with ConfigUtils.ImplicitConv
@Test def testApply: Unit = {
ConfigTest.config("m1", Nil, "k1").asString shouldBe "v2"
ConfigTest.config("m1", Nil, "notexist", default = "default").asString shouldBe "default"
- intercept[IllegalStateException] {
- ConfigTest.config("m1", Nil, "notexist")
- }
}
@Test def testMergeConfigs: Unit = {
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
index 1b493f2e14df822b75534fed3722f88917882fe1..19940fde2ecb2c923cdbed79b9fcb85bd1ab4e39 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
@@ -11,10 +11,10 @@ import org.testng.annotations.Test
*/
class ConfigurableTest extends TestNGSuite with Matchers {
@Test def testConfigurable: Unit = {
- Config.global.map = Map()
- Config.global.loadConfigFile(ConfigurableTest.file)
-
- val classC = new ClassC
+ val classC = new ClassC {
+ override def configName = "classc"
+ override val globalConfig = new Config(ConfigurableTest.map)
+ }
classC.configPath shouldBe Nil
classC.configFullPath shouldBe List("classc")
@@ -27,10 +27,6 @@ class ConfigurableTest extends TestNGSuite with Matchers {
classC.classB.get("k1").asString shouldBe "c1"
classC.classB.classA.get("k1").asString shouldBe "c1"
- classC.get("notexist") shouldBe null
- intercept[IllegalStateException] {
- classC.get("notexist", required = true)
- }
classC.get("notexist", default = "default").asString shouldBe "default"
classC.get("k1", freeVar = false).asString shouldBe "c1"
@@ -47,23 +43,24 @@ abstract class Cfg extends Configurable {
def get(key: String,
default: String = null,
submodule: String = null,
- required: Boolean = false,
freeVar: Boolean = true,
sample: String = null,
library: String = null) = {
- config(key, default, submodule, required, freeVar = freeVar, sample = sample, library = library)
+ config(key, default, submodule, freeVar = freeVar, sample = sample, library = library)
}
}
class ClassA(val root: Configurable) extends Cfg
class ClassB(val root: Configurable) extends Cfg {
- val classA = new ClassA(this)
+ lazy val classA = new ClassA(this)
+ // Why this needs to be lazy?
}
class ClassC(val root: Configurable) extends Cfg {
def this() = this(null)
- val classB = new ClassB(this)
+ lazy val classB = new ClassB(this)
+ // Why this needs to be lazy?
}
object ConfigurableTest {
@@ -85,6 +82,4 @@ object ConfigurableTest {
)
)
)
-
- val file = ConfigUtilsTest.writeTemp(ConfigUtils.mapToJson(map).spaces2)
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
index 1c98a36f2698d23806aa48de151b4cffa20eb056..6c9db2d2144df792d5ca97558cd1a9737377f1cb 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
@@ -30,187 +30,229 @@ class FastqSyncTest extends TestNGSuite with MockitoSugar with Matchers {
.map(x => new FastqRecord(x, "A", "", "H"))
.toIterator.asJava
- @DataProvider(name = "mockReaderProvider")
- def mockReaderProvider() =
+ @DataProvider(name = "mockProvider")
+ def mockProvider() =
Array(
- Array(mock[FastqReader], mock[FastqReader], mock[FastqReader]))
+ Array(mock[FastqReader], mock[FastqReader], mock[FastqReader],
+ mock[AsyncFastqWriter], mock[AsyncFastqWriter])
+ )
+
+ @Test(dataProvider = "mockProvider")
+ def testDefault(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader,
+ aOutMock: AsyncFastqWriter, bOutMock: AsyncFastqWriter) = {
- @Test(dataProvider = "mockReaderProvider")
- def testDefault(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader) = {
when(refMock.iterator) thenReturn recordsOver("1", "2", "3")
when(aMock.iterator) thenReturn recordsOver("1", "2", "3")
when(bMock.iterator) thenReturn recordsOver("1", "2", "3")
+ val obs = inOrd(aOutMock, bOutMock)
+ val exp = recordsOver("1", "2", "3").asScala.toSeq
+
+ val (numDiscard1, numDiscard2, numKept) = syncFastq(refMock, aMock, bMock, aOutMock, bOutMock)
+
+ obs.verify(aOutMock).write(exp(0))
+ obs.verify(bOutMock).write(exp(0))
+
+ obs.verify(aOutMock).write(exp(1))
+ obs.verify(bOutMock).write(exp(1))
+
+ obs.verify(aOutMock).write(exp(2))
+ obs.verify(bOutMock).write(exp(2))
- val (sync, counts) = syncFastq(refMock, aMock, bMock)
- sync.length shouldBe 3
- sync(0) shouldBe (new FastqRecord("1", "A", "", "H"), new FastqRecord("1", "A", "", "H"))
- sync(1) shouldBe (new FastqRecord("2", "A", "", "H"), new FastqRecord("2", "A", "", "H"))
- sync(2) shouldBe (new FastqRecord("3", "A", "", "H"), new FastqRecord("3", "A", "", "H"))
- counts.numDiscard1 shouldBe 0
- counts.numDiscard2 shouldBe 0
- counts.numKept shouldBe 3
+ numDiscard1 shouldBe 0
+ numDiscard2 shouldBe 0
+ numKept shouldBe 3
}
- @Test(dataProvider = "mockReaderProvider")
- def testRefTooShort(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader) = {
+ @Test(dataProvider = "mockProvider")
+ def testRefTooShort(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader,
+ aOutMock: AsyncFastqWriter, bOutMock: AsyncFastqWriter) = {
+
when(refMock.iterator) thenReturn recordsOver("1", "2")
when(aMock.iterator) thenReturn recordsOver("1", "2", "3")
when(bMock.iterator) thenReturn recordsOver("1", "2", "3")
val thrown = intercept[NoSuchElementException] {
- syncFastq(refMock, aMock, bMock)
+ syncFastq(refMock, aMock, bMock, aOutMock, bOutMock)
}
thrown.getMessage should ===("Reference record stream shorter than expected")
}
- @Test(dataProvider = "mockReaderProvider")
- def testSeqAEmpty(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader) = {
+ @Test(dataProvider = "mockProvider")
+ def testSeqAEmpty(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader,
+ aOutMock: AsyncFastqWriter, bOutMock: AsyncFastqWriter) = {
+
when(refMock.iterator) thenReturn recordsOver("1", "2", "3")
when(aMock.iterator) thenReturn recordsOver()
when(bMock.iterator) thenReturn recordsOver("1", "2", "3")
- val (sync, counts) = syncFastq(refMock, aMock, bMock)
- sync.length shouldBe 0
- counts.numDiscard1 shouldBe 0
- counts.numDiscard2 shouldBe 3
- counts.numKept shouldBe 0
+ val (numDiscard1, numDiscard2, numKept) = syncFastq(refMock, aMock, bMock, aOutMock, bOutMock)
+
+ numDiscard1 shouldBe 0
+ numDiscard2 shouldBe 3
+ numKept shouldBe 0
}
- @Test(dataProvider = "mockReaderProvider")
- def testSeqBEmpty(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader) = {
+ @Test(dataProvider = "mockProvider")
+ def testSeqBEmpty(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader,
+ aOutMock: AsyncFastqWriter, bOutMock: AsyncFastqWriter) = {
+
when(refMock.iterator) thenReturn recordsOver("1", "2", "3")
when(aMock.iterator) thenReturn recordsOver("1", "2", "3")
when(bMock.iterator) thenReturn recordsOver()
- val (sync, counts) = syncFastq(refMock, aMock, bMock)
- sync.length shouldBe 0
- counts.numDiscard1 shouldBe 3
- counts.numDiscard2 shouldBe 0
- counts.numKept shouldBe 0
+ val (numDiscard1, numDiscard2, numKept) = syncFastq(refMock, aMock, bMock, aOutMock, bOutMock)
+
+ numDiscard1 shouldBe 3
+ numDiscard2 shouldBe 0
+ numKept shouldBe 0
}
- @Test(dataProvider = "mockReaderProvider")
- def testSeqAShorter(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader) = {
+ @Test(dataProvider = "mockProvider")
+ def testSeqAShorter(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader,
+ aOutMock: AsyncFastqWriter, bOutMock: AsyncFastqWriter) = {
+
when(refMock.iterator) thenReturn recordsOver("1", "2", "3")
when(aMock.iterator) thenReturn recordsOver("2", "3")
when(bMock.iterator) thenReturn recordsOver("1", "2", "3")
+ val obs = inOrd(aOutMock, bOutMock)
+ val exp = recordsOver("1", "2", "3").asScala.toSeq
+
+ val (numDiscard1, numDiscard2, numKept) = syncFastq(refMock, aMock, bMock, aOutMock, bOutMock)
+
+ // exp(0) is discarded by syncFastq
+ obs.verify(aOutMock).write(exp(1))
+ obs.verify(bOutMock).write(exp(1))
- val (sync, counts) = syncFastq(refMock, aMock, bMock)
- sync.length shouldBe 2
- sync(0) shouldBe (new FastqRecord("2", "A", "", "H"), new FastqRecord("2", "A", "", "H"))
- sync(1) shouldBe (new FastqRecord("3", "A", "", "H"), new FastqRecord("3", "A", "", "H"))
- counts.numDiscard1 shouldBe 0
- counts.numDiscard2 shouldBe 1
- counts.numKept shouldBe 2
+ obs.verify(aOutMock).write(exp(2))
+ obs.verify(bOutMock).write(exp(2))
+
+ numDiscard1 shouldBe 0
+ numDiscard2 shouldBe 1
+ numKept shouldBe 2
}
- @Test(dataProvider = "mockReaderProvider")
- def testSeqBShorter(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader) = {
+ @Test(dataProvider = "mockProvider")
+ def testSeqBShorter(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader,
+ aOutMock: AsyncFastqWriter, bOutMock: AsyncFastqWriter) = {
+
when(refMock.iterator) thenReturn recordsOver("1", "2", "3")
- when(aMock.iterator) thenReturn recordsOver("2", "3")
- when(bMock.iterator) thenReturn recordsOver("1", "2", "3")
+ when(aMock.iterator) thenReturn recordsOver("1", "2", "3")
+ when(bMock.iterator) thenReturn recordsOver("1", "3")
+ val obs = inOrd(aOutMock, bOutMock)
+ val exp = recordsOver("1", "2", "3").asScala.toSeq
+
+ val (numDiscard1, numDiscard2, numKept) = syncFastq(refMock, aMock, bMock, aOutMock, bOutMock)
- val (sync, counts) = syncFastq(refMock, aMock, bMock)
- sync.length shouldBe 2
- sync(0) shouldBe (new FastqRecord("2", "A", "", "H"), new FastqRecord("2", "A", "", "H"))
- sync(1) shouldBe (new FastqRecord("3", "A", "", "H"), new FastqRecord("3", "A", "", "H"))
- counts.numDiscard1 shouldBe 0
- counts.numDiscard2 shouldBe 1
- counts.numKept shouldBe 2
+ // exp(1) is discarded by syncFastq
+ obs.verify(aOutMock).write(exp(0))
+ obs.verify(bOutMock).write(exp(0))
+
+ obs.verify(aOutMock).write(exp(2))
+ obs.verify(bOutMock).write(exp(2))
+
+ numDiscard1 shouldBe 1
+ numDiscard2 shouldBe 0
+ numKept shouldBe 2
}
- @Test(dataProvider = "mockReaderProvider")
- def testSeqABShorter(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader) = {
+ @Test(dataProvider = "mockProvider")
+ def testSeqABShorter(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader,
+ aOutMock: AsyncFastqWriter, bOutMock: AsyncFastqWriter) = {
+
when(refMock.iterator) thenReturn recordsOver("1", "2", "3")
when(aMock.iterator) thenReturn recordsOver("2", "3")
when(bMock.iterator) thenReturn recordsOver("1", "2")
+ val obs = inOrd(aOutMock, bOutMock)
+ val exp = recordsOver("1", "2", "3").asScala.toSeq
+
+ val (numDiscard1, numDiscard2, numKept) = syncFastq(refMock, aMock, bMock, aOutMock, bOutMock)
+
+ // exp(0) and exp(2) are discarded by syncFastq
+ obs.verify(aOutMock).write(exp(1))
+ obs.verify(bOutMock).write(exp(1))
- val (sync, counts) = syncFastq(refMock, aMock, bMock)
- sync.length shouldBe 1
- sync(0) shouldBe (new FastqRecord("2", "A", "", "H"), new FastqRecord("2", "A", "", "H"))
- counts.numDiscard1 shouldBe 1
- counts.numDiscard2 shouldBe 1
- counts.numKept shouldBe 1
+ numDiscard1 shouldBe 1
+ numDiscard2 shouldBe 1
+ numKept shouldBe 1
}
- @Test(dataProvider = "mockReaderProvider")
- def testSeqABShorterPairMarkSlash(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader) = {
+ @Test(dataProvider = "mockProvider")
+ def testSeqABShorterPairMarkSlash(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader,
+ aOutMock: AsyncFastqWriter, bOutMock: AsyncFastqWriter) = {
+
when(refMock.iterator) thenReturn recordsOver("1/1", "2/1", "3/1")
when(aMock.iterator) thenReturn recordsOver("2/1", "3/1")
when(bMock.iterator) thenReturn recordsOver("1/2", "2/2")
+ val obs = inOrd(aOutMock, bOutMock)
+
+ val (numDiscard1, numDiscard2, numKept) = syncFastq(refMock, aMock, bMock, aOutMock, bOutMock)
+
+ obs.verify(aOutMock).write(new FastqRecord("2/1", "A", "", "H"))
+ obs.verify(bOutMock).write(new FastqRecord("2/2", "A", "", "H"))
- val (sync, counts) = syncFastq(refMock, aMock, bMock)
- sync.length shouldBe 1
- sync(0) shouldBe (new FastqRecord("2/1", "A", "", "H"), new FastqRecord("2/2", "A", "", "H"))
- counts.numDiscard1 shouldBe 1
- counts.numDiscard2 shouldBe 1
- counts.numKept shouldBe 1
+ numDiscard1 shouldBe 1
+ numDiscard2 shouldBe 1
+ numKept shouldBe 1
}
- @Test(dataProvider = "mockReaderProvider")
- def testSeqABShorterPairMarkUnderscore(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader) = {
+ @Test(dataProvider = "mockProvider")
+ def testSeqABShorterPairMarkUnderscore(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader,
+ aOutMock: AsyncFastqWriter, bOutMock: AsyncFastqWriter) = {
+
when(refMock.iterator) thenReturn recordsOver("1_1", "2_1", "3_1")
when(aMock.iterator) thenReturn recordsOver("2_1", "3_1")
when(bMock.iterator) thenReturn recordsOver("1_2", "2_2")
+ val obs = inOrd(aOutMock, bOutMock)
+
+ val (numDiscard1, numDiscard2, numKept) = syncFastq(refMock, aMock, bMock, aOutMock, bOutMock)
- val (sync, counts) = syncFastq(refMock, aMock, bMock)
- sync.length shouldBe 1
- sync(0) shouldBe (new FastqRecord("2_1", "A", "", "H"), new FastqRecord("2_2", "A", "", "H"))
- counts.numDiscard1 shouldBe 1
- counts.numDiscard2 shouldBe 1
- counts.numKept shouldBe 1
+ obs.verify(aOutMock).write(new FastqRecord("2_1", "A", "", "H"))
+ obs.verify(bOutMock).write(new FastqRecord("2_2", "A", "", "H"))
+
+ numDiscard1 shouldBe 1
+ numDiscard2 shouldBe 1
+ numKept shouldBe 1
}
- @Test(dataProvider = "mockReaderProvider")
- def testSeqABShorterWithDesc(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader) = {
+ @Test(dataProvider = "mockProvider")
+ def testSeqABShorterWithDescription(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader,
+ aOutMock: AsyncFastqWriter, bOutMock: AsyncFastqWriter) = {
+
when(refMock.iterator) thenReturn recordsOver("1 desc1b", "2 desc2b", "3 desc3b")
when(aMock.iterator) thenReturn recordsOver("2 desc2a", "3 desc3a")
when(bMock.iterator) thenReturn recordsOver("1 desc1b", "2 desc2b")
+ val obs = inOrd(aOutMock, bOutMock)
+
+ val (numDiscard1, numDiscard2, numKept) = syncFastq(refMock, aMock, bMock, aOutMock, bOutMock)
- val (sync, counts) = syncFastq(refMock, aMock, bMock)
- sync.length shouldBe 1
- sync(0) shouldBe (new FastqRecord("2 desc2a", "A", "", "H"), new FastqRecord("2 desc2b", "A", "", "H"))
- counts.numDiscard1 shouldBe 1
- counts.numDiscard2 shouldBe 1
- counts.numKept shouldBe 1
+ obs.verify(aOutMock).write(new FastqRecord("2 desc2a", "A", "", "H"))
+ obs.verify(bOutMock).write(new FastqRecord("2 desc2b", "A", "", "H"))
+
+ numDiscard1 shouldBe 1
+ numDiscard2 shouldBe 1
+ numKept shouldBe 1
}
- @Test(dataProvider = "mockReaderProvider")
- def testComplex(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader) = {
+ @Test(dataProvider = "mockProvider")
+ def testComplex(refMock: FastqReader, aMock: FastqReader, bMock: FastqReader,
+ aOutMock: AsyncFastqWriter, bOutMock: AsyncFastqWriter) = {
+
when(refMock.iterator) thenReturn recordsOver("1/2 yep", "2/2 yep", "3/2 yep", "4/2 yep", "5/2 yep")
when(aMock.iterator) thenReturn recordsOver("1/1 yep", "2/1 yep", "4/1 yep")
when(bMock.iterator) thenReturn recordsOver("1/2 yep", "3/2 yep", "4/2 yep")
+ val obs = inOrd(aOutMock, bOutMock)
- val (sync, counts) = syncFastq(refMock, aMock, bMock)
- sync.length shouldBe 2
- sync(0) shouldBe (new FastqRecord("1/1 yep", "A", "", "H"), new FastqRecord("1/2 yep", "A", "", "H"))
- sync(1) shouldBe (new FastqRecord("4/1 yep", "A", "", "H"), new FastqRecord("4/2 yep", "A", "", "H"))
- counts.numDiscard1 shouldBe 1
- counts.numDiscard2 shouldBe 1
- counts.numKept shouldBe 2
- }
+ val (numDiscard1, numDiscard2, numKept) = syncFastq(refMock, aMock, bMock, aOutMock, bOutMock)
- @Test def testWriteSynced() = {
- val aMock = mock[AsyncFastqWriter]
- val bMock = mock[AsyncFastqWriter]
- val sync = Stream(
- (new FastqRecord("1", "A", "", "H"), new FastqRecord("1", "T", "", "E")),
- (new FastqRecord("2", "A", "", "H"), new FastqRecord("2", "T", "", "E")))
- val counts = SyncCounts(4, 3, 2)
- val obs = inOrd(aMock, bMock)
- val stdout = new java.io.ByteArrayOutputStream
- Console.withOut(stdout) {
- writeSyncedFastq(sync, counts, aMock, bMock)
- }
- stdout.toString should ===(List(
- "Filtered 4 reads from first read file.",
- "Filtered 3 reads from second read file.",
- "Synced read files contain 2 reads.\n"
- ).mkString("\n"))
- obs.verify(aMock).write(new FastqRecord("1", "A", "", "H"))
- obs.verify(bMock).write(new FastqRecord("1", "T", "", "E"))
- obs.verify(aMock).write(new FastqRecord("2", "A", "", "H"))
- obs.verify(bMock).write(new FastqRecord("2", "T", "", "E"))
+ obs.verify(aOutMock).write(new FastqRecord("1/1 yep", "A", "", "H"))
+ obs.verify(bOutMock).write(new FastqRecord("1/2 yep", "A", "", "H"))
+
+ obs.verify(aOutMock).write(new FastqRecord("4/1 yep", "A", "", "H"))
+ obs.verify(bOutMock).write(new FastqRecord("4/2 yep", "A", "", "H"))
+
+ numDiscard1 shouldBe 1
+ numDiscard2 shouldBe 1
+ numKept shouldBe 2
}
@Test def testArgsMinimum() = {
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
index 26f989c5369c4e138ded82620d1d03f0c076ce7c..3a53f91f0462a27d81d3dd83a449f94c1d31d514 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
@@ -6,7 +6,6 @@ import argonaut.Argonaut._
import argonaut.Json
import nl.lumc.sasc.biopet.core.config.{ ConfigValueIndex, ConfigValue }
import org.scalatest.Matchers
-import org.scalatest.mock.MockitoSugar
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
@@ -170,79 +169,23 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
val index = ConfigValueIndex("test", Nil, "test")
new ImplicitConversions {
configValue2list(ConfigValue(index, index, List(""))) shouldBe List("")
- intercept[IllegalStateException] {
- configValue2list(ConfigValue(index, index, null))
- }
-
configValue2stringList(ConfigValue(index, index, List(""))) shouldBe List("")
- intercept[IllegalStateException] {
- configValue2stringList(ConfigValue(index, index, null))
- }
-
configValue2stringSet(ConfigValue(index, index, List(""))) shouldBe Set("")
- intercept[IllegalStateException] {
- configValue2stringSet(ConfigValue(index, index, null))
- }
var int: Int = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- int = ConfigValue(index, index, null)
- }
-
var long: Long = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- long = ConfigValue(index, index, null)
- }
-
var double: Double = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- double = ConfigValue(index, index, null)
- }
-
var float: Float = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- float = ConfigValue(index, index, null)
- }
-
var boolean: Boolean = ConfigValue(index, index, true)
- intercept[IllegalStateException] {
- boolean = ConfigValue(index, index, null)
- }
-
var intOption: Option[Int] = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- int = ConfigValue(index, index, null)
- }
-
var longOption: Option[Long] = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- long = ConfigValue(index, index, null)
- }
-
var doubleOption: Option[Double] = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- double = ConfigValue(index, index, null)
- }
-
var floatOption: Option[Float] = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- float = ConfigValue(index, index, null)
- }
-
var booleanOption: Option[Boolean] = ConfigValue(index, index, true)
- intercept[IllegalStateException] {
- boolean = ConfigValue(index, index, null)
- }
-
var string: String = ConfigValue(index, index, "test")
- intercept[IllegalStateException] {
- string = ConfigValue(index, index, null)
- }
-
var file: File = ConfigValue(index, index, "test")
- intercept[IllegalStateException] {
- file = ConfigValue(index, index, null)
- }
+
+ //TODO: test BiopetQScript error message
}
}
}
diff --git a/public/biopet-public-package/BiopetPublicPackage.iml b/public/biopet-public-package/BiopetPublicPackage.iml
deleted file mode 100644
index c83b2a2ec98305049f75d2ac582879b20eba447e..0000000000000000000000000000000000000000
--- a/public/biopet-public-package/BiopetPublicPackage.iml
+++ /dev/null
@@ -1,99 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="false">
- <output url="file://$MODULE_DIR$/target/classes" />
- <output-test url="file://$MODULE_DIR$/target/test-classes" />
- <content url="file://$MODULE_DIR$">
- <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
- <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
- <excludeFolder url="file://$MODULE_DIR$/target" />
- </content>
- <orderEntry type="inheritedJdk" />
- <orderEntry type="sourceFolder" forTests="false" />
- <orderEntry type="module" module-name="BiopetFramework" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" />
- <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" />
- <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" />
- <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" />
- <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" />
- <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" />
- <orderEntry type="module-library">
- <library name="Maven: com.sun:tools:1.4.2">
- <CLASSES>
- <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" />
- </CLASSES>
- <JAVADOC />
- <SOURCES />
- </library>
- </orderEntry>
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" />
- <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" />
- <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" />
- <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" />
- <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" />
- <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" />
- <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" />
- <orderEntry type="module-library">
- <library name="Maven: com.sun:tools.jar:1.5">
- <CLASSES>
- <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" />
- </CLASSES>
- <JAVADOC />
- <SOURCES />
- </library>
- </orderEntry>
- <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" />
- <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" />
- <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" />
- <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" />
- <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" />
- <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" />
- <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
- <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" />
- <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
- <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" />
- <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" />
- <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" />
- <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" />
- <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" />
- <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" />
- <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" />
- <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" />
- <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
- <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" />
- <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" />
- <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" />
- <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" />
- <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" />
- <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" />
- <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" />
- <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" />
- <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" />
- <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" />
- <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" />
- <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" />
- <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" />
- <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" />
- <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" />
- <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" />
- <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" />
- <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
- <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" />
- <orderEntry type="module" module-name="Flexiprep" />
- <orderEntry type="module" module-name="Mapping" />
- <orderEntry type="module" module-name="BamMetrics" />
- <orderEntry type="module" module-name="Gentrap" />
- <orderEntry type="module" module-name="Sage" />
- <orderEntry type="module" module-name="Yamsvp" />
- <orderEntry type="module" module-name="Toucan" />
- </component>
-</module>
\ No newline at end of file
diff --git a/public/biopet-public-package/pom.xml b/public/biopet-public-package/pom.xml
index 12e31dad57fe487d238cea749213f78449cf79fb..2b30d7f259d7b0d1d23c95caa510dcfa630b2010 100644
--- a/public/biopet-public-package/pom.xml
+++ b/public/biopet-public-package/pom.xml
@@ -80,6 +80,11 @@
<artifactId>Kopisu</artifactId>
<version>${project.version}</version>
</dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>Bam2Wig</artifactId>
+ <version>${project.version}</version>
+ </dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Carp</artifactId>
diff --git a/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala b/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
index dbc3f5b1686c57e5dcf763fa4c603a7fe62edcdc..0b50590c8ede10500214877b2057d219082ee853 100644
--- a/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
+++ b/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
@@ -23,6 +23,7 @@ object BiopetExecutablePublic extends BiopetExecutable {
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics,
nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp,
nl.lumc.sasc.biopet.pipelines.sage.Sage,
+ nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig,
nl.lumc.sasc.biopet.pipelines.kopisu.ConiferPipeline,
nl.lumc.sasc.biopet.pipelines.carp.Carp,
nl.lumc.sasc.biopet.pipelines.toucan.Toucan
diff --git a/public/biopet-public-package/src/test/resources/log4j.properties b/public/biopet-public-package/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/public/biopet-public-package/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/public/carp/pom.xml b/public/carp/pom.xml
index 482b83147312cf332cc7325c6a9196c092dcd91a..e6e0f86fc2bfed50f8361ccd18f450c84f3b2158 100644
--- a/public/carp/pom.xml
+++ b/public/carp/pom.xml
@@ -44,5 +44,17 @@
<artifactId>Mapping</artifactId>
<version>${project.version}</version>
</dependency>
+ <dependency>
+ <groupId>org.testng</groupId>
+ <artifactId>testng</artifactId>
+ <version>6.8</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.scalatest</groupId>
+ <artifactId>scalatest_2.11</artifactId>
+ <version>2.2.1</version>
+ <scope>test</scope>
+ </dependency>
</dependencies>
</project>
diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
index 578f3afc79f6cac8d2621399bb577222383ee2bb..6868704b3d35dc8ef9fde30a02fdb009cd9c74a8 100644
--- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+++ b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
@@ -20,6 +20,7 @@ import java.io.File
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
import nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
+import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input }
@@ -38,7 +39,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
def this() = this(null)
override def defaults = ConfigUtils.mergeMaps(Map(
- "mapping" -> Map("skip_markduplicates" -> true)
+ "mapping" -> Map("skip_markduplicates" -> true, "aligner" -> "bwa")
), super.defaults)
def makeSample(id: String) = new Sample(id)
@@ -80,10 +81,10 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
merge.sortOrder = "coordinate"
merge.output = bamFile
add(merge)
-
- //TODO: Add BigWIg track
}
+ addAll(Bam2Wig(qscript, bamFile).functions)
+
val macs2 = new Macs2CallPeak(qscript)
macs2.treatment = bamFile
macs2.name = Some(sampleId)
diff --git a/public/carp/src/test/resources/log4j.properties b/public/carp/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/public/carp/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala b/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..fd57a752a0039cd69eccf93dd6bb805eae1ebc86
--- /dev/null
+++ b/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
@@ -0,0 +1,147 @@
+package nl.lumc.sasc.biopet.pipelines.carp
+
+import java.io.File
+
+import com.google.common.io.Files
+import org.apache.commons.io.FileUtils
+import org.broadinstitute.gatk.queue.QSettings
+import org.testng.annotations.{ AfterClass, Test, DataProvider }
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+
+import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
+import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
+import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, SortSam }
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+
+/**
+ * Created by pjvan_thof on 2/13/15.
+ */
+class CarpTest extends TestNGSuite with Matchers {
+ def initPipeline(map: Map[String, Any]): Carp = {
+ new Carp() {
+ override def configName = "carp"
+ override def globalConfig = new Config(map)
+ qSettings = new QSettings
+ qSettings.runName = "test"
+ }
+ }
+
+ @DataProvider(name = "carpOptions", parallel = true)
+ def carpOptions = {
+ val bool = Array(true, false)
+
+ for (s1 <- bool; s2 <- bool; s3 <- bool; t <- bool; c <- bool) yield Array("", s1, s2, s3, t, c)
+ }
+
+ @Test(dataProvider = "carpOptions")
+ def testCarp(f: String, sample1: Boolean, sample2: Boolean, sample3: Boolean, threatment: Boolean, control: Boolean): Unit = {
+ val map = {
+ var m = ConfigUtils.mergeMaps(Map("output_dir" -> CarpTest.outputDir
+ ), CarpTest.excutables)
+
+ if (sample1) m = ConfigUtils.mergeMaps(CarpTest.sample1, m.toMap)
+ if (sample2) m = ConfigUtils.mergeMaps(CarpTest.sample2, m.toMap)
+ if (sample3) m = ConfigUtils.mergeMaps(CarpTest.sample3, m.toMap)
+ if (threatment) m = ConfigUtils.mergeMaps(CarpTest.threatment1, m.toMap)
+ if (control) m = ConfigUtils.mergeMaps(CarpTest.control1, m.toMap)
+ m
+ }
+
+ if (!sample1 && !sample2 && !sample3 && !threatment && !control) { // When no samples
+ intercept[IllegalArgumentException] {
+ initPipeline(map).script()
+ }
+ } else if (threatment && !control) { // If control of a samples does not exist in samples
+ intercept[IllegalStateException] {
+ initPipeline(map).script()
+ }
+ } else { // When samples are correct
+ val carp = initPipeline(map)
+ carp.script()
+ val numberLibs = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 2 else 0) +
+ (if (threatment) 1 else 0) + (if (control) 1 else 0)
+ val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 1 else 0) +
+ (if (threatment) 1 else 0) + (if (control) 1 else 0)
+
+ carp.functions.count(_.isInstanceOf[BwaMem]) shouldBe numberLibs
+ carp.functions.count(_.isInstanceOf[SortSam]) shouldBe numberLibs
+ carp.functions.count(_.isInstanceOf[MergeSamFiles]) shouldBe (if (sample3) 1 else 0)
+
+ carp.functions.count(_.isInstanceOf[Macs2CallPeak]) shouldBe (numberSamples + (if (threatment) 1 else 0))
+ }
+ }
+
+ // remove temporary run directory all tests in the class have been run
+ @AfterClass def removeTempOutputDir() = {
+ FileUtils.deleteDirectory(CarpTest.outputDir)
+ }
+}
+
+object CarpTest {
+ val outputDir = Files.createTempDir()
+
+ val excutables = Map(
+ "reference" -> "test",
+ "seqstat" -> Map("exe" -> "test"),
+ "fastqc" -> Map("exe" -> "test"),
+ "seqtk" -> Map("exe" -> "test"),
+ "sickle" -> Map("exe" -> "test"),
+ "bwa" -> Map("exe" -> "test"),
+ "samtools" -> Map("exe" -> "test"),
+ "macs2" -> Map("exe" -> "test"),
+ "igvtools" -> Map("exe" -> "test"),
+ "wigtobigwig" -> Map("exe" -> "test")
+ )
+
+ val sample1 = Map(
+ "samples" -> Map("sample1" -> Map("libraries" -> Map(
+ "lib1" -> Map(
+ "R1" -> "1_1_R1.fq",
+ "R2" -> "1_1_R2.fq"
+ )
+ )
+ )))
+
+ val sample2 = Map(
+ "samples" -> Map("sample2" -> Map("libraries" -> Map(
+ "lib1" -> Map(
+ "R1" -> "2_1_R1.fq",
+ "R2" -> "2_1_R2.fq"
+ )
+ )
+ )))
+
+ val sample3 = Map(
+ "samples" -> Map("sample3" -> Map("libraries" -> Map(
+ "lib1" -> Map(
+ "R1" -> "3_1_R1.fq",
+ "R2" -> "3_1_R2.fq"
+ ),
+ "lib2" -> Map(
+ "R1" -> "3_2_R1.fq",
+ "R2" -> "3_2_R2.fq"
+ )
+ )
+ )))
+
+ val threatment1 = Map(
+ "samples" -> Map("threatment" -> Map("control" -> "control1", "libraries" -> Map(
+ "lib1" -> Map(
+ "R1" -> "threatment_1_R1.fq",
+ "R2" -> "threatment_1_R2.fq"
+ )
+ )
+ )))
+
+ val control1 = Map(
+ "samples" -> Map("control1" -> Map("libraries" -> Map(
+ "lib1" -> Map(
+ "R1" -> "control_1_R1.fq",
+ "R2" -> "control_1_R2.fq"
+ )
+ )
+ )))
+
+}
\ No newline at end of file
diff --git a/public/flexiprep/Flexiprep.iml b/public/flexiprep/Flexiprep.iml
deleted file mode 100644
index dc0afbee2ccf2f185458a930863b52ade6962739..0000000000000000000000000000000000000000
--- a/public/flexiprep/Flexiprep.iml
+++ /dev/null
@@ -1,92 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="false">
- <output url="file://$MODULE_DIR$/target/classes" />
- <output-test url="file://$MODULE_DIR$/target/test-classes" />
- <content url="file://$MODULE_DIR$">
- <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
- <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
- <excludeFolder url="file://$MODULE_DIR$/target" />
- </content>
- <orderEntry type="inheritedJdk" />
- <orderEntry type="sourceFolder" forTests="false" />
- <orderEntry type="module" module-name="BiopetFramework" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" />
- <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" />
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- <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" />
- <orderEntry type="module-library">
- <library name="Maven: com.sun:tools:1.4.2">
- <CLASSES>
- <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" />
- </CLASSES>
- <JAVADOC />
- <SOURCES />
- </library>
- </orderEntry>
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" />
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- <CLASSES>
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- <JAVADOC />
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- <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" />
- <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" />
- <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" />
- <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" />
- <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" />
- <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" />
- <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" />
- <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" />
- <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" />
- <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" />
- <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" />
- <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" />
- <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" />
- <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" />
- <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
- <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" />
- </component>
-</module>
\ No newline at end of file
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
index 50ee00b2c5625226a00e0985bbe761ded375237c..46e2107ddcc8aa33d8efc9aca5d36e4207e3cbc1 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
@@ -52,10 +52,7 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
* @throws FileNotFoundException if the FastQC data file can not be found.
* @throws IllegalStateException if the module lines have no content or mapping is empty.
*/
- @throws(classOf[FileNotFoundException])
- @throws(classOf[IllegalStateException])
def qcModules: Map[String, FastQCModule] = {
-
val fqModules = Source.fromFile(dataFile)
// drop all the characters before the first module delimiter (i.e. '>>')
.dropWhile(_ != '>')
@@ -93,14 +90,16 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
* @throws NoSuchElementException when the "Basic Statistics" key does not exist in the mapping or
* when a line starting with "Encoding" does not exist.
*/
- @throws(classOf[NoSuchElementException])
- def encoding: String =
- qcModules("Basic Statistics")
- .lines
- .dropWhile(!_.startsWith("Encoding"))
- .head
- .stripPrefix("Encoding\t")
- .stripSuffix("\t")
+ def encoding: String = {
+ if (dataFile.exists) // On a dry run this file does not yet exist
+ qcModules("Basic Statistics") //FIXME: not save
+ .lines
+ .dropWhile(!_.startsWith("Encoding"))
+ .head
+ .stripPrefix("Encoding\t")
+ .stripSuffix("\t")
+ else ""
+ }
/** Case class representing a known adapter sequence */
protected case class AdapterSequence(name: String, seq: String)
@@ -111,32 +110,33 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
* @return a [[Set]] of [[AdapterSequence]] objects.
*/
def foundAdapters: Set[AdapterSequence] = {
+ if (dataFile.exists) { // On a dry run this file does not yet exist
+ /** Returns a list of adapter and/or contaminant sequences known to FastQC */
+ def getFastqcSeqs(file: Option[File]): Set[AdapterSequence] = file match {
+ case None => Set.empty[AdapterSequence]
+ case Some(f) =>
+ (for {
+ line <- Source.fromFile(f).getLines()
+ if !line.startsWith("#")
+ values = line.split("\t+")
+ if values.size >= 2
+ } yield AdapterSequence(values(0), values(1))).toSet
+ }
+
+ val found = qcModules.get("Overrepresented sequences") match {
+ case None => Seq.empty[String]
+ case Some(qcModule) =>
+ for (
+ line <- qcModule.lines if !(line.startsWith("#") || line.startsWith(">"));
+ values = line.split("\t") if values.size >= 4
+ ) yield values(3)
+ }
- /** Returns a list of adapter and/or contaminant sequences known to FastQC */
- def getFastqcSeqs(file: Option[File]): Set[AdapterSequence] = file match {
- case None => Set.empty[AdapterSequence]
- case Some(f) =>
- (for {
- line <- Source.fromFile(f).getLines()
- if !line.startsWith("#")
- values = line.split("\t+")
- if values.size >= 2
- } yield AdapterSequence(values(0), values(1))).toSet
- }
-
- val found = qcModules.get("Overrepresented sequences") match {
- case None => Seq.empty[String]
- case Some(qcModule) =>
- for (
- line <- qcModule.lines if !(line.startsWith("#") || line.startsWith(">"));
- values = line.split("\t") if values.size >= 4
- ) yield values(3)
- }
-
- // select full sequences from known adapters and contaminants
- // based on overrepresented sequences results
- (getFastqcSeqs(adapters) ++ getFastqcSeqs(contaminants))
- .filter(x => found.exists(_.startsWith(x.name)))
+ // select full sequences from known adapters and contaminants
+ // based on overrepresented sequences results
+ (getFastqcSeqs(adapters) ++ getFastqcSeqs(contaminants))
+ .filter(x => found.exists(_.startsWith(x.name)))
+ } else Set()
}
/** Summary of the FastQC run, stored in a [[Json]] object */
@@ -164,7 +164,7 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
object Fastqc {
- def apply(root: Configurable, fastqfile: File, outDir: String): Fastqc = {
+ def apply(root: Configurable, fastqfile: File, outDir: File): Fastqc = {
val fastqcCommand = new Fastqc(root)
fastqcCommand.fastqfile = fastqfile
var filename: String = fastqfile.getName()
@@ -172,8 +172,8 @@ object Fastqc {
if (filename.endsWith(".gzip")) filename = filename.substring(0, filename.size - 5)
if (filename.endsWith(".fastq")) filename = filename.substring(0, filename.size - 6)
//if (filename.endsWith(".fq")) filename = filename.substring(0,filename.size - 3)
- fastqcCommand.output = new File(outDir + "/" + filename + "_fastqc.zip")
- fastqcCommand.afterGraph
+ fastqcCommand.output = new File(outDir, filename + "_fastqc.zip")
+ fastqcCommand.beforeGraph
fastqcCommand
}
}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 9ab16032bd095d40728e91f92a611366b400af2f..95e41f8ff6b1b86acb5cb4a3490373d4e1503698 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -87,7 +87,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
case _ =>
}
- summary.out = outputDir + sampleId + "-" + libId + ".qc.summary.json"
+ summary.out = new File(outputDir, sampleId + "-" + libId + ".qc.summary.json")
}
def biopetScript() {
@@ -105,7 +105,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
outputFiles += ("fastq_input_R1" -> extractIfNeeded(input_R1, outputDir))
if (paired) outputFiles += ("fastq_input_R2" -> extractIfNeeded(input_R2.get, outputDir))
- fastqc_R1 = Fastqc(this, input_R1, outputDir + "/" + R1_name + ".fastqc/")
+ fastqc_R1 = Fastqc(this, input_R1, new File(outputDir, R1_name + ".fastqc/"))
add(fastqc_R1)
summary.addFastqc(fastqc_R1)
outputFiles += ("fastqc_R1" -> fastqc_R1.output)
@@ -115,7 +115,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
summary.addMd5sum(md5sum_R1, R2 = false, after = false)
if (paired) {
- fastqc_R2 = Fastqc(this, input_R2.get, outputDir + "/" + R2_name + ".fastqc/")
+ fastqc_R2 = Fastqc(this, input_R2.get, new File(outputDir, R2_name + ".fastqc/"))
add(fastqc_R2)
summary.addFastqc(fastqc_R2, R2 = true)
outputFiles += ("fastqc_R2" -> fastqc_R2.output)
@@ -126,16 +126,16 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
}
}
- def runTrimClip(R1_in: File, outDir: String, chunk: String): (File, File, List[File]) = {
+ def runTrimClip(R1_in: File, outDir: File, chunk: String): (File, File, List[File]) = {
runTrimClip(R1_in, new File(""), outDir, chunk)
}
- def runTrimClip(R1_in: File, outDir: String): (File, File, List[File]) = {
+ def runTrimClip(R1_in: File, outDir: File): (File, File, List[File]) = {
runTrimClip(R1_in, new File(""), outDir, "")
}
- def runTrimClip(R1_in: File, R2_in: File, outDir: String): (File, File, List[File]) = {
+ def runTrimClip(R1_in: File, R2_in: File, outDir: File): (File, File, List[File]) = {
runTrimClip(R1_in, R2_in, outDir, "")
}
- def runTrimClip(R1_in: File, R2_in: File, outDir: String, chunkarg: String): (File, File, List[File]) = {
+ def runTrimClip(R1_in: File, R2_in: File, outDir: File, chunkarg: String): (File, File, List[File]) = {
val chunk = if (chunkarg.isEmpty || chunkarg.endsWith("_")) chunkarg else chunkarg + "_"
var results: Map[String, File] = Map()
@@ -245,8 +245,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
def runFinalize(fastq_R1: List[File], fastq_R2: List[File]) {
if (fastq_R1.length != fastq_R2.length && paired) throw new IllegalStateException("R1 and R2 file number is not the same")
- val R1 = new File(outputDir + R1_name + ".qc" + R1_ext + ".gz")
- val R2 = new File(outputDir + R2_name + ".qc" + R2_ext + ".gz")
+ val R1 = new File(outputDir, R1_name + ".qc" + R1_ext + ".gz")
+ val R2 = new File(outputDir, R2_name + ".qc" + R2_ext + ".gz")
add(Gzip(this, fastq_R1, R1))
if (paired) add(Gzip(this, fastq_R2, R2))
@@ -263,11 +263,11 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
add(md5sum_R2)
summary.addMd5sum(md5sum_R2, R2 = true, after = true)
}
- fastqc_R1_after = Fastqc(this, R1, outputDir + "/" + R1_name + ".qc.fastqc/")
+ fastqc_R1_after = Fastqc(this, R1, new File(outputDir, R1_name + ".qc.fastqc/"))
add(fastqc_R1_after)
summary.addFastqc(fastqc_R1_after, after = true)
if (paired) {
- fastqc_R2_after = Fastqc(this, R2, outputDir + "/" + R2_name + ".qc.fastqc/")
+ fastqc_R2_after = Fastqc(this, R2, new File(outputDir, R2_name + ".qc.fastqc/"))
add(fastqc_R2_after)
summary.addFastqc(fastqc_R2_after, R2 = true, after = true)
}
@@ -276,7 +276,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
add(summary)
}
- def extractIfNeeded(file: File, runDir: String): File = {
+ def extractIfNeeded(file: File, runDir: File): File = {
if (file == null) return file
else if (file.getName().endsWith(".gz") || file.getName().endsWith(".gzip")) {
var newFile: File = swapExt(runDir, file, ".gz", "")
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
index 0fdeee289de9672d917264e3e9dc2d556f6bc48b..03144feee45b395504864abfadff03e50713429d 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
@@ -27,17 +27,18 @@ class SeqtkSeq(root: Configurable) extends nl.lumc.sasc.biopet.extensions.seqtk.
if (fastqc != null && Q == None) {
val encoding = fastqc.encoding
Q = encoding match {
- case null => None
+ case null => None
case s if (s.contains("Sanger / Illumina 1.9")) => None
- case s if (s.contains("Illumina <1.3")) => Option(64)
- case s if (s.contains("Illumina 1.3")) => Option(64)
- case s if (s.contains("Illumina 1.5")) => Option(64)
+ case s if (s.contains("Illumina <1.3")) => Option(64)
+ case s if (s.contains("Illumina 1.3")) => Option(64)
+ case s if (s.contains("Illumina 1.5")) => Option(64)
+ case _ => None
}
if (Q != None) V = true
}
}
- override def afterGraph {
+ override def beforeGraph {
if (fastqc != null) deps ::= fastqc.output
}
diff --git a/public/flexiprep/src/test/resources/log4j.properties b/public/flexiprep/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/public/flexiprep/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..7f6c81a342c3266ea95626677d345f28eec6201c
--- /dev/null
+++ b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
@@ -0,0 +1,88 @@
+package nl.lumc.sasc.biopet.pipelines.flexiprep
+
+import java.io.File
+
+import com.google.common.io.Files
+import org.apache.commons.io.FileUtils
+import org.broadinstitute.gatk.queue.QSettings
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.{ AfterClass, DataProvider, Test }
+
+import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.extensions.{ Gzip, Zcat }
+import nl.lumc.sasc.biopet.tools.FastqSync
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+
+/**
+ * Created by pjvan_thof on 2/11/15.
+ */
+class FlexiprepTest extends TestNGSuite with Matchers {
+
+ def initPipeline(map: Map[String, Any]): Flexiprep = {
+ new Flexiprep() {
+ override def configName = "flexiprep"
+ override def globalConfig = new Config(map)
+ qSettings = new QSettings
+ qSettings.runName = "test"
+ }
+ }
+
+ @DataProvider(name = "flexiprepOptions", parallel = true)
+ def flexiprepOptions = {
+ val paired = Array(true, false)
+ val skipTrims = Array(true, false)
+ val skipClips = Array(true, false)
+ val zipped = Array(true, false)
+
+ for (
+ pair <- paired;
+ skipTrim <- skipTrims;
+ skipClip <- skipClips;
+ zip <- zipped
+ ) yield Array("", pair, skipTrim, skipClip, zip)
+ }
+
+ @Test(dataProvider = "flexiprepOptions")
+ def testFlexiprep(f: String, paired: Boolean, skipTrim: Boolean, skipClip: Boolean, zipped: Boolean) = {
+ val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir,
+ "skip_trim" -> skipTrim,
+ "skip_clip" -> skipClip
+ ), Map(FlexiprepTest.excutables.toSeq: _*))
+ val flexiprep: Flexiprep = initPipeline(map)
+
+ flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq" + (if (zipped) ".gz" else ""))
+ if (paired) flexiprep.input_R2 = Some(new File(flexiprep.outputDir, "bla_R2.fq" + (if (zipped) ".gz" else "")))
+ flexiprep.sampleId = "1"
+ flexiprep.libId = "1"
+ flexiprep.script()
+
+ flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe (
+ if (paired && (skipClip && skipTrim)) 2
+ else if (!paired && (skipClip && skipTrim)) 1
+ else if (paired && !(skipClip && skipTrim)) 4
+ else if (!paired && !(skipClip && skipTrim)) 2)
+ flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe (if (zipped) (if (paired) 2 else 1) else 0)
+ flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe (if (paired) 2 else 1)
+ flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe (if (skipClip) 0 else (if (paired) 2 else 1))
+ flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe (if (skipClip) 0 else (if (paired) 1 else 0))
+ flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe (if (skipTrim) 0 else 1)
+ flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe (if (paired) 2 else 1)
+ }
+
+ // remove temporary run directory all tests in the class have been run
+ @AfterClass def removeTempOutputDir() = {
+ FileUtils.deleteDirectory(FlexiprepTest.outputDir)
+ }
+}
+
+object FlexiprepTest {
+ val outputDir = Files.createTempDir()
+
+ val excutables = Map(
+ "seqstat" -> Map("exe" -> "test"),
+ "fastqc" -> Map("exe" -> "test"),
+ "seqtk" -> Map("exe" -> "test"),
+ "sickle" -> Map("exe" -> "test")
+ )
+}
\ No newline at end of file
diff --git a/public/gentrap/Gentrap.iml b/public/gentrap/Gentrap.iml
deleted file mode 100644
index e1eb4b5603b6bdbe4340c36aa195798b205535db..0000000000000000000000000000000000000000
--- a/public/gentrap/Gentrap.iml
+++ /dev/null
@@ -1,95 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="false">
- <output url="file://$MODULE_DIR$/target/classes" />
- <output-test url="file://$MODULE_DIR$/target/test-classes" />
- <content url="file://$MODULE_DIR$">
- <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
- <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
- <excludeFolder url="file://$MODULE_DIR$/target" />
- </content>
- <orderEntry type="inheritedJdk" />
- <orderEntry type="sourceFolder" forTests="false" />
- <orderEntry type="module" module-name="BiopetFramework" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" />
- <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" />
- <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" />
- <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" />
- <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" />
- <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" />
- <orderEntry type="module-library">
- <library name="Maven: com.sun:tools:1.4.2">
- <CLASSES>
- <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" />
- </CLASSES>
- <JAVADOC />
- <SOURCES />
- </library>
- </orderEntry>
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" />
- <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" />
- <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" />
- <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" />
- <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" />
- <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" />
- <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" />
- <orderEntry type="module-library">
- <library name="Maven: com.sun:tools.jar:1.5">
- <CLASSES>
- <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" />
- </CLASSES>
- <JAVADOC />
- <SOURCES />
- </library>
- </orderEntry>
- <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" />
- <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" />
- <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" />
- <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" />
- <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" />
- <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" />
- <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
- <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" />
- <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
- <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" />
- <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" />
- <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" />
- <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" />
- <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" />
- <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" />
- <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" />
- <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" />
- <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
- <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" />
- <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" />
- <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" />
- <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" />
- <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" />
- <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" />
- <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" />
- <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" />
- <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" />
- <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" />
- <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" />
- <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" />
- <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" />
- <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" />
- <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" />
- <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" />
- <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" />
- <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
- <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" />
- <orderEntry type="module" module-name="Mapping" />
- <orderEntry type="module" module-name="Flexiprep" />
- <orderEntry type="module" module-name="BamMetrics" />
- </component>
-</module>
\ No newline at end of file
diff --git a/public/gentrap/src/test/resources/log4j.properties b/public/gentrap/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/public/gentrap/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
index c45de4eac904af6b110c7448416d0ce0a90fe8e3..5e935517233bffe3f4d3d8ef46e5fded98d6a5bf 100644
--- a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
+++ b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.kopisu
-import java.io.{ BufferedWriter, FileWriter, File }
+import java.io.{ FileFilter, BufferedWriter, FileWriter, File }
import nl.lumc.sasc.biopet.core.{ PipelineCommand, _ }
import nl.lumc.sasc.biopet.core.config._
@@ -80,17 +80,23 @@ class ConiferPipeline(val root: Configurable) extends QScript with BiopetQScript
val coniferRPKM = new ConiferRPKM(this)
coniferRPKM.bamFile = this.inputBam.getAbsoluteFile
coniferRPKM.probes = this.probeFile
- coniferRPKM.output = new File(RPKMdir + File.separator + input2RPKM(inputBam))
+ coniferRPKM.output = new File(RPKMdir, input2RPKM(inputBam))
add(coniferRPKM)
if (!RPKMonly) {
/** Collect the rpkm_output to a temp directory, where we merge with the control files */
var refRPKMlist: List[File] = Nil
- for (f <- controlsDir.listFiles()) {
- var target = new File(RPKMdir + File.separator + f.getName)
- if (!target.exists()) {
- logger.info("Creating " + target.getAbsolutePath)
- add(Ln(this, f, target, true))
+ // Sync the .txt only, these files contain the RPKM Values
+ for (controlRPKMfile <- controlsDir.list.filter(_.toLowerCase.endsWith(".txt"))) {
+ val target = new File(RPKMdir, controlRPKMfile)
+ val source = new File(controlsDir, controlRPKMfile)
+
+ if (!target.exists) {
+ add(Ln(this, source, target, false))
+ refRPKMlist :+= target
+ } else if (!target.equals(source)) {
+ target.delete()
+ add(Ln(this, source, target, false))
refRPKMlist :+= target
}
}
@@ -99,18 +105,18 @@ class ConiferPipeline(val root: Configurable) extends QScript with BiopetQScript
coniferAnalyze.deps = List(coniferRPKM.output) ++ refRPKMlist
coniferAnalyze.probes = this.probeFile
coniferAnalyze.rpkmDir = RPKMdir
- coniferAnalyze.output = new File(sampleDir + File.separator + input2HDF5(inputBam))
+ coniferAnalyze.output = new File(sampleDir, input2HDF5(inputBam))
add(coniferAnalyze)
val coniferCall = new ConiferCall(this)
coniferCall.input = coniferAnalyze.output
- coniferCall.output = new File(sampleDir + File.separator + "calls.txt")
+ coniferCall.output = new File(sampleDir, "calls.txt")
add(coniferCall)
summary.deps = List(coniferCall.output)
summary.label = sampleLabel
summary.calls = coniferCall.output
- summary.out = new File(sampleDir + File.separator + input2Calls(inputBam))
+ summary.out = new File(sampleDir, input2Calls(inputBam))
add(summary)
}
diff --git a/public/kopisu/src/test/resources/log4j.properties b/public/kopisu/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/public/kopisu/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/public/mapping/Mapping.iml b/public/mapping/Mapping.iml
deleted file mode 100644
index c76cc7f3bf70d48923f895e158c35dbd72b6af78..0000000000000000000000000000000000000000
--- a/public/mapping/Mapping.iml
+++ /dev/null
@@ -1,94 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="false">
- <output url="file://$MODULE_DIR$/target/classes" />
- <output-test url="file://$MODULE_DIR$/target/test-classes" />
- <content url="file://$MODULE_DIR$">
- <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
- <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
- <excludeFolder url="file://$MODULE_DIR$/target" />
- </content>
- <orderEntry type="inheritedJdk" />
- <orderEntry type="sourceFolder" forTests="false" />
- <orderEntry type="module" module-name="BiopetFramework" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" />
- <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" />
- <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" />
- <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" />
- <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" />
- <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" />
- <orderEntry type="module-library">
- <library name="Maven: com.sun:tools:1.4.2">
- <CLASSES>
- <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" />
- </CLASSES>
- <JAVADOC />
- <SOURCES />
- </library>
- </orderEntry>
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" />
- <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" />
- <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" />
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- <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" />
- <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" />
- <orderEntry type="module-library">
- <library name="Maven: com.sun:tools.jar:1.5">
- <CLASSES>
- <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" />
- </CLASSES>
- <JAVADOC />
- <SOURCES />
- </library>
- </orderEntry>
- <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" />
- <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" />
- <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" />
- <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" />
- <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" />
- <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" />
- <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
- <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" />
- <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
- <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" />
- <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" />
- <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" />
- <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" />
- <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" />
- <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" />
- <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" />
- <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" />
- <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
- <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" />
- <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" />
- <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" />
- <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" />
- <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" />
- <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" />
- <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" />
- <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" />
- <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" />
- <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" />
- <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" />
- <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" />
- <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" />
- <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" />
- <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" />
- <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" />
- <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" />
- <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
- <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" />
- <orderEntry type="module" module-name="Flexiprep" />
- <orderEntry type="module" module-name="BamMetrics" />
- </component>
-</module>
\ No newline at end of file
diff --git a/public/mapping/pom.xml b/public/mapping/pom.xml
index 345678a7a642580cb2a733d6c90239633efdea5b..71d0de73f7a4e6cda61bd668628b19776e929fe9 100644
--- a/public/mapping/pom.xml
+++ b/public/mapping/pom.xml
@@ -49,5 +49,22 @@
<artifactId>BamMetrics</artifactId>
<version>${project.version}</version>
</dependency>
+ <dependency>
+ <groupId>org.testng</groupId>
+ <artifactId>testng</artifactId>
+ <version>6.8</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.scalatest</groupId>
+ <artifactId>scalatest_2.11</artifactId>
+ <version>2.2.1</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>Bam2Wig</artifactId>
+ <version>${project.version}</version>
+ </dependency>
</dependencies>
</project>
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 9094d38cddbe70d8c7b6787200d2afe94e19d486..e6e483ab4b24cf2146c23946d12932f41021b269 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -21,6 +21,7 @@ import java.util.Date
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.{ Ln, Star, Stampy, Bowtie }
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaSamse, BwaSampe, BwaAln, BwaMem }
+import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import nl.lumc.sasc.biopet.tools.FastqSplitter
import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, SortSam, MergeSamFiles, AddOrReplaceReadGroups }
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
@@ -96,7 +97,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
protected var paired: Boolean = false
val flexiprep = new Flexiprep(this)
- def finalBamFile: File = outputDir + outputName + ".final.bam"
+ def finalBamFile: File = new File(outputDir, outputName + ".final.bam")
def init() {
require(outputDir != null, "Missing output directory on mapping module")
@@ -127,7 +128,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
def biopetScript() {
if (!skipFlexiprep) {
- flexiprep.outputDir = outputDir + "flexiprep" + File.separator
+ flexiprep.outputDir = new File(outputDir, "flexiprep")
flexiprep.input_R1 = input_R1
flexiprep.input_R2 = input_R2
flexiprep.sampleId = this.sampleId
@@ -144,9 +145,9 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
else if (file.endsWith(".gzip")) return file.substring(0, file.lastIndexOf(".gzip"))
else return file
}
- var chunks: Map[String, (String, String)] = Map()
+ var chunks: Map[File, (String, String)] = Map()
if (chunking) for (t <- 1 to numberChunks.getOrElse(1)) {
- val chunkDir = outputDir + "chunks/" + t + "/"
+ val chunkDir = new File(outputDir, "chunks" + File.separator + t)
chunks += (chunkDir -> (removeGz(chunkDir + input_R1.getName),
if (paired) removeGz(chunkDir + input_R2.get.getName) else ""))
}
@@ -176,7 +177,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
var R2 = fastqfile._2
var deps: List[File] = Nil
if (!skipFlexiprep) {
- val flexiout = flexiprep.runTrimClip(R1, R2, chunkDir + "flexiprep/", chunkDir)
+ val flexiout = flexiprep.runTrimClip(R1, R2, new File(chunkDir, "flexiprep"), chunkDir)
logger.debug(chunkDir + " - " + flexiout)
R1 = flexiout._1
if (paired) R2 = flexiout._2
@@ -185,7 +186,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
fastq_R2_output :+= R2
}
- val outputBam = new File(chunkDir + outputName + ".bam")
+ val outputBam = new File(chunkDir, outputName + ".bam")
bamFiles :+= outputBam
aligner match {
case "bwa" => addBwaMem(R1, R2, outputBam, deps)
@@ -197,7 +198,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
case _ => throw new IllegalStateException("Option Aligner: '" + aligner + "' is not valid")
}
if (config("chunk_metrics", default = false))
- addAll(BamMetrics(this, outputBam, chunkDir + "metrics/").functions)
+ addAll(BamMetrics(this, outputBam, new File(chunkDir, "metrics")).functions)
}
if (!skipFlexiprep) {
flexiprep.runFinalize(fastq_R1_output, fastq_R2_output)
@@ -206,7 +207,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
var bamFile = bamFiles.head
if (!skipMarkduplicates) {
- bamFile = new File(outputDir + outputName + ".dedup.bam")
+ bamFile = new File(outputDir, outputName + ".dedup.bam")
add(MarkDuplicates(this, bamFiles, bamFile))
} else if (skipMarkduplicates && chunking) {
val mergeSamFile = MergeSamFiles(this, bamFiles, outputDir)
@@ -214,11 +215,14 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
bamFile = mergeSamFile.output
}
- if (!skipMetrics) addAll(BamMetrics(this, bamFile, outputDir + "metrics" + File.separator).functions)
+ if (!skipMetrics) addAll(BamMetrics(this, bamFile, new File(outputDir, "metrics")).functions)
add(Ln(this, swapExt(outputDir, bamFile, ".bam", ".bai"), swapExt(outputDir, finalBamFile, ".bam", ".bai")))
add(Ln(this, bamFile, finalBamFile))
outputFiles += ("finalBamFile" -> bamFile)
+
+ if (config("generate_wig", default = false).asBoolean)
+ addAll(Bam2Wig(this, finalBamFile).functions)
}
def addBwaAln(R1: File, R2: File, output: File, deps: List[File]): File = {
diff --git a/public/mapping/src/test/resources/log4j.properties b/public/mapping/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/public/mapping/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..19b773aba8155eb5773cef5ebc567ae7638b5956
--- /dev/null
+++ b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
@@ -0,0 +1,122 @@
+package nl.lumc.sasc.biopet.pipelines.mapping
+
+import java.io.File
+
+import com.google.common.io.Files
+import org.apache.commons.io.FileUtils
+import org.broadinstitute.gatk.queue.QSettings
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.{ AfterClass, DataProvider, Test }
+
+import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.extensions.bwa.{ BwaSamse, BwaSampe, BwaAln, BwaMem }
+import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, AddOrReplaceReadGroups, MarkDuplicates, SortSam }
+import nl.lumc.sasc.biopet.extensions._
+import nl.lumc.sasc.biopet.pipelines.flexiprep.Cutadapt
+import nl.lumc.sasc.biopet.pipelines.flexiprep.Fastqc
+import nl.lumc.sasc.biopet.pipelines.flexiprep.Sickle
+import nl.lumc.sasc.biopet.pipelines.flexiprep._
+import nl.lumc.sasc.biopet.tools.FastqSync
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+
+/**
+ * Created by pjvan_thof on 2/12/15.
+ */
+class MappingTest extends TestNGSuite with Matchers {
+ def initPipeline(map: Map[String, Any]): Mapping = {
+ new Mapping {
+ override def configName = "mapping"
+ override def globalConfig = new Config(map)
+ qSettings = new QSettings
+ qSettings.runName = "test"
+ }
+ }
+
+ @DataProvider(name = "mappingOptions", parallel = true)
+ def mappingOptions = {
+ val aligners = Array("bwa", "bwa-aln", "star", "star-2pass", "bowtie", "stampy")
+ val paired = Array(true, false)
+ val chunks = Array(1, 5, 10, 100)
+ val skipMarkDuplicates = Array(true, false)
+ val skipFlexipreps = Array(true, false)
+
+ for (
+ aligner <- aligners;
+ pair <- paired;
+ chunk <- chunks;
+ skipMarkDuplicate <- skipMarkDuplicates;
+ skipFlexiprep <- skipFlexipreps
+ ) yield Array(aligner, pair, chunk, skipMarkDuplicate, skipFlexiprep)
+ }
+
+ @Test(dataProvider = "mappingOptions")
+ def testMapping(aligner: String, paired: Boolean, chunks: Int, skipMarkDuplicate: Boolean, skipFlexiprep: Boolean) = {
+ val map = ConfigUtils.mergeMaps(Map("output_dir" -> MappingTest.outputDir,
+ "aligner" -> aligner,
+ "number_chunks" -> chunks,
+ "skip_markduplicates" -> skipMarkDuplicate,
+ "skip_flexiprep" -> skipFlexiprep
+ ), Map(MappingTest.excutables.toSeq: _*))
+ val mapping: Mapping = initPipeline(map)
+
+ mapping.input_R1 = new File(mapping.outputDir, "bla_R1.fq")
+ if (paired) mapping.input_R2 = Some(new File(mapping.outputDir, "bla_R2.fq"))
+ mapping.sampleId = "1"
+ mapping.libId = "1"
+ mapping.script()
+
+ //Flexiprep
+ mapping.functions.count(_.isInstanceOf[Fastqc]) shouldBe (if (skipFlexiprep) 0 else if (paired) 4 else 2)
+ mapping.functions.count(_.isInstanceOf[Zcat]) shouldBe 0
+ mapping.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe ((if (skipFlexiprep) 0 else if (paired) 2 else 1) * chunks)
+ mapping.functions.count(_.isInstanceOf[Cutadapt]) shouldBe ((if (skipFlexiprep) 0 else if (paired) 2 else 1) * chunks)
+ mapping.functions.count(_.isInstanceOf[FastqSync]) shouldBe ((if (skipFlexiprep) 0 else if (paired && !skipFlexiprep) 1 else 0) * chunks)
+ mapping.functions.count(_.isInstanceOf[Sickle]) shouldBe ((if (skipFlexiprep) 0 else 1) * chunks)
+ mapping.functions.count(_.isInstanceOf[Gzip]) shouldBe (if (skipFlexiprep) 0 else if (paired) 2 else 1)
+
+ //aligners
+ mapping.functions.count(_.isInstanceOf[BwaMem]) shouldBe ((if (aligner == "bwa") 1 else 0) * chunks)
+ mapping.functions.count(_.isInstanceOf[BwaAln]) shouldBe ((if (aligner == "bwa-aln") (if (paired) 2 else 1) else 0) * chunks)
+ mapping.functions.count(_.isInstanceOf[BwaSampe]) shouldBe ((if (aligner == "bwa-aln") (if (paired) 1 else 0) else 0) * chunks)
+ mapping.functions.count(_.isInstanceOf[BwaSamse]) shouldBe ((if (aligner == "bwa-aln") (if (paired) 0 else 1) else 0) * chunks)
+ mapping.functions.count(_.isInstanceOf[Star]) shouldBe ((if (aligner == "star") 1 else if (aligner == "star-2pass") 3 else 0) * chunks)
+ mapping.functions.count(_.isInstanceOf[Bowtie]) shouldBe ((if (aligner == "bowtie") 1 else 0) * chunks)
+ mapping.functions.count(_.isInstanceOf[Stampy]) shouldBe ((if (aligner == "stampy") 1 else 0) * chunks)
+
+ // Sort sam or replace readgroup
+ val sort = aligner match {
+ case "bwa" | "bwa-aln" | "stampy" => "sortsam"
+ case "star" | "star-2pass" | "bowtie" => "replacereadgroups"
+ case _ => throw new IllegalArgumentException("aligner: " + aligner + " does not exist")
+ }
+
+ mapping.functions.count(_.isInstanceOf[SortSam]) shouldBe ((if (sort == "sortsam") 1 else 0) * chunks)
+ mapping.functions.count(_.isInstanceOf[AddOrReplaceReadGroups]) shouldBe ((if (sort == "replacereadgroups") 1 else 0) * chunks)
+
+ mapping.functions.count(_.isInstanceOf[MergeSamFiles]) shouldBe (if (skipMarkDuplicate && chunks > 1) 1 else 0)
+ mapping.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (if (skipMarkDuplicate) 0 else 1)
+ }
+
+ // remove temporary run directory all tests in the class have been run
+ @AfterClass def removeTempOutputDir() = {
+ FileUtils.deleteDirectory(MappingTest.outputDir)
+ }
+}
+
+object MappingTest {
+ val outputDir = Files.createTempDir()
+
+ val excutables = Map(
+ "reference" -> "test",
+ "seqstat" -> Map("exe" -> "test"),
+ "fastqc" -> Map("exe" -> "test"),
+ "seqtk" -> Map("exe" -> "test"),
+ "sickle" -> Map("exe" -> "test"),
+ "bwa" -> Map("exe" -> "test"),
+ "star" -> Map("exe" -> "test"),
+ "bowtie" -> Map("exe" -> "test"),
+ "stampy" -> Map("exe" -> "test", "genome" -> "test", "hash" -> "test"),
+ "samtools" -> Map("exe" -> "test")
+ )
+}
\ No newline at end of file
diff --git a/public/pom.xml b/public/pom.xml
index 2820c83511f6d05d1989ef8b0fec97a0214d0d9b..be14eaf353ba25868a7e2d47edb7170cfeb2fc8a 100644
--- a/public/pom.xml
+++ b/public/pom.xml
@@ -34,6 +34,7 @@
<module>sage</module>
<module>kopisu</module>
<module>yamsvp</module>
+ <module>bam2wig</module>
<module>carp</module>
<module>toucan</module>
</modules>
diff --git a/public/sage/Sage.iml b/public/sage/Sage.iml
deleted file mode 100644
index e1eb4b5603b6bdbe4340c36aa195798b205535db..0000000000000000000000000000000000000000
--- a/public/sage/Sage.iml
+++ /dev/null
@@ -1,95 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="false">
- <output url="file://$MODULE_DIR$/target/classes" />
- <output-test url="file://$MODULE_DIR$/target/test-classes" />
- <content url="file://$MODULE_DIR$">
- <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
- <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
- <excludeFolder url="file://$MODULE_DIR$/target" />
- </content>
- <orderEntry type="inheritedJdk" />
- <orderEntry type="sourceFolder" forTests="false" />
- <orderEntry type="module" module-name="BiopetFramework" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" />
- <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" />
- <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" />
- <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" />
- <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" />
- <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" />
- <orderEntry type="module-library">
- <library name="Maven: com.sun:tools:1.4.2">
- <CLASSES>
- <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" />
- </CLASSES>
- <JAVADOC />
- <SOURCES />
- </library>
- </orderEntry>
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" />
- <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" />
- <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" />
- <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" />
- <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" />
- <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" />
- <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" />
- <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" />
- <orderEntry type="module-library">
- <library name="Maven: com.sun:tools.jar:1.5">
- <CLASSES>
- <root url="jar:///usr/lib/jvm/java-7-openjdk-amd64/lib/tools.jar!/" />
- </CLASSES>
- <JAVADOC />
- <SOURCES />
- </library>
- </orderEntry>
- <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" />
- <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" />
- <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" />
- <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" />
- <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" />
- <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" />
- <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
- <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" />
- <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
- <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" />
- <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" />
- <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" />
- <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" />
- <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" />
- <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" />
- <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" />
- <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" />
- <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
- <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" />
- <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" />
- <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" />
- <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" />
- <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" />
- <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" />
- <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" />
- <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" />
- <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" />
- <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" />
- <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" />
- <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" />
- <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" />
- <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" />
- <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" />
- <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" />
- <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" />
- <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
- <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" />
- <orderEntry type="module" module-name="Mapping" />
- <orderEntry type="module" module-name="Flexiprep" />
- <orderEntry type="module" module-name="BamMetrics" />
- </component>
-</module>
\ No newline at end of file
diff --git a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
index ed55ca382d13346b3cbb7bb4862941ef4da591f5..f510bf8e5756bf2ffc18460339b7580d2e2ccdf6 100644
--- a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+++ b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
@@ -15,6 +15,8 @@
*/
package nl.lumc.sasc.biopet.pipelines.sage
+import java.io.File
+
import nl.lumc.sasc.biopet.core.{ BiopetQScript, MultiSampleQScript, PipelineCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.Cat
@@ -60,7 +62,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
class Sample(sampleId: String) extends AbstractSample(sampleId) {
def makeLibrary(id: String) = new Library(id)
class Library(libId: String) extends AbstractLibrary(libId) {
- val inputFastq: File = config("R1", required = true)
+ val inputFastq: File = config("R1")
val prefixFastq: File = createFile(".prefix.fastq")
val flexiprep = new Flexiprep(qscript)
@@ -72,7 +74,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
mapping.sampleId = sampleId
protected def addJobs(): Unit = {
- flexiprep.outputDir = libDir + "flexiprep/"
+ flexiprep.outputDir = new File(libDir, "flexiprep/")
flexiprep.input_R1 = inputFastq
flexiprep.init
flexiprep.biopetScript
@@ -123,7 +125,6 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
}
def init() {
- if (!outputDir.endsWith("/")) outputDir += "/"
if (transcriptome.isEmpty && tagsLibrary.isEmpty)
throw new IllegalStateException("No transcriptome or taglib found")
if (countBed.isEmpty)
@@ -138,10 +139,10 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
if (tagsLibrary.isEmpty) {
val cdl = new SageCreateLibrary(this)
cdl.input = transcriptome.get
- cdl.output = outputDir + "taglib/tag.lib"
- cdl.noAntiTagsOutput = outputDir + "taglib/no_antisense_genes.txt"
- cdl.noTagsOutput = outputDir + "taglib/no_sense_genes.txt"
- cdl.allGenesOutput = outputDir + "taglib/all_genes.txt"
+ cdl.output = new File(outputDir, "taglib/tag.lib")
+ cdl.noAntiTagsOutput = new File(outputDir, "taglib/no_antisense_genes.txt")
+ cdl.noTagsOutput = new File(outputDir, "taglib/no_sense_genes.txt")
+ cdl.allGenesOutput = new File(outputDir, "taglib/all_genes.txt")
add(cdl)
tagsLibrary = Some(cdl.output)
}
diff --git a/public/sage/src/test/resources/log4j.properties b/public/sage/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/public/sage/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/public/yamsvp/Yamsvp.iml b/public/yamsvp/Yamsvp.iml
deleted file mode 100644
index e1eb4b5603b6bdbe4340c36aa195798b205535db..0000000000000000000000000000000000000000
--- a/public/yamsvp/Yamsvp.iml
+++ /dev/null
@@ -1,95 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="false">
- <output url="file://$MODULE_DIR$/target/classes" />
- <output-test url="file://$MODULE_DIR$/target/test-classes" />
- <content url="file://$MODULE_DIR$">
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\ No newline at end of file
diff --git a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
index 206c92a69453105fb2034d6cd72cce00f5ab75cd..6e7257c7d94967eac350fc212e7c7b37ebf5dc58 100644
--- a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
+++ b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
@@ -35,7 +35,7 @@ import org.broadinstitute.gatk.queue.engine.JobRunInfo
class Yamsvp(val root: Configurable) extends QScript with BiopetQScript { //with MultiSampleQScript {
def this() = this(null)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
var finalBamFiles: List[File] = Nil
/*
class LibraryOutput extends AbstractLibraryOutput {
diff --git a/public/yamsvp/src/test/resources/log4j.properties b/public/yamsvp/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/public/yamsvp/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file