Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
b0774761
Commit
b0774761
authored
Mar 16, 2015
by
bow
Browse files
Merge branch 'release-0.3.0'
parents
19d495c5
25d3f569
Changes
391
Hide whitespace changes
Inline
Side-by-side
.gitignore
View file @
b0774761
...
...
@@ -7,7 +7,8 @@ git.properties
# Vim
*.swp
# IntelliJ
.idea/workspace.xml
/target/
/public/target/
/protected/target/
.idea/*
*.iml
target/
public/target/
protected/target/
.idea/compiler.xml
deleted
100644 → 0
View file @
19d495c5
<?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=
"true"
>
<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>
\ No newline at end of file
.idea/copyright/profiles_settings.xml
deleted
100644 → 0
View file @
19d495c5
<component
name=
"CopyrightManager"
>
<settings
default=
""
/>
</component>
\ No newline at end of file
.idea/encodings.xml
deleted
100644 → 0
View file @
19d495c5
<?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>
\ No newline at end of file
.idea/libraries/Maven__colt_colt_1_2_0.xml
deleted
100644 → 0
View file @
19d495c5
<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
.idea/libraries/Maven__com_beust_jcommander_1_27.xml
deleted
100644 → 0
View file @
19d495c5
<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
.idea/libraries/Maven__com_github_julien_truffaut_monocle_core_2_11_0_5_0.xml
deleted
100644 → 0
View file @
19d495c5
<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
.idea/libraries/Maven__com_github_scopt_scopt_2_10_3_2_0.xml
deleted
100644 → 0
View file @
19d495c5
<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
.idea/libraries/Maven__com_google_code_cofoja_cofoja_1_0_r139.xml
deleted
100644 → 0
View file @
19d495c5
<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
.idea/libraries/Maven__com_google_code_gson_gson_2_2_2.xml
deleted
100644 → 0
View file @
19d495c5
<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
.idea/libraries/Maven__com_google_guava_guava_18_0.xml
deleted
100644 → 0
View file @
19d495c5
<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
.idea/libraries/Maven__com_jamesmurty_utils_java_xmlbuilder_0_4.xml
deleted
100644 → 0
View file @
19d495c5
<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
.idea/libraries/Maven__commons_codec_commons_codec_1_3.xml
deleted
100644 → 0
View file @
19d495c5
<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
.idea/libraries/Maven__commons_collections_commons_collections_3_2_1.xml
deleted
100644 → 0
View file @
19d495c5
<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
.idea/libraries/Maven__commons_httpclient_commons_httpclient_3_1.xml
deleted
100644 → 0
View file @
19d495c5
<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
.idea/libraries/Maven__commons_io_commons_io_2_1.xml
deleted
100644 → 0
View file @
19d495c5
<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
.idea/libraries/Maven__commons_lang_commons_lang_2_5.xml
deleted
100644 → 0
View file @
19d495c5
<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
.idea/libraries/Maven__commons_logging_commons_logging_1_1_1.xml
deleted
100644 → 0
View file @
19d495c5
<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
.idea/libraries/Maven__concurrent_concurrent_1_3_4.xml
deleted
100644 → 0
View file @
19d495c5
<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
.idea/libraries/Maven__dom4j_dom4j_1_6_1.xml
deleted
100644 → 0
View file @
19d495c5
<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
Prev
1
2
3
4
5
…
20
Next
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment