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Commit 25a8538c authored by Peter van 't Hof's avatar Peter van 't Hof
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Merge branch 'feature-wipereads' into 'develop' 

Feature wipereads

The main update here is to use `com.google.guava` for BloomFilter as it works fine with OpenJDK7 (the one that GATK uses internally). This means the pom.xml file has also been updated. As this is mainly for GATK 3.3 dependency, I've also updated the IntelliJ project file.

See merge request !21
parents 5dd7125a e960e5db
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.idea/libraries/Maven__com_baqend_bloom_filter_1_02.xml deleted 100644 → 0
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− 13
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<component name="libraryTable">
<library name="Maven: com.baqend:bloom-filter:1.02">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/com/baqend/bloom-filter/1.02/bloom-filter-1.02.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/com/baqend/bloom-filter/1.02/bloom-filter-1.02-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/com/baqend/bloom-filter/1.02/bloom-filter-1.02-sources.jar!/" />
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__com_google_code_gson_gson_2_2_4.xml deleted 100644 → 0
+ 0
− 13
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<component name="libraryTable">
<library name="Maven: com.google.code.gson:gson:2.2.4">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/com/google/code/gson/gson/2.2.4/gson-2.2.4.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/com/google/code/gson/gson/2.2.4/gson-2.2.4-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/com/google/code/gson/gson/2.2.4/gson-2.2.4-sources.jar!/" />
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__com_google_guava_guava_17_0.xml → .idea/libraries/Maven__com_google_guava_guava_18_0.xml
+ 4
− 4
View file @ 25a8538c
<component name="libraryTable"> <component name="libraryTable">
<library name="Maven: com.google.guava:guava:17.0"> <library name="Maven: com.google.guava:guava:18.0">
<CLASSES> <CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/com/google/guava/guava/17.0/guava-17.0.jar!/" /> <root url="jar://$MAVEN_REPOSITORY$/com/google/guava/guava/18.0/guava-18.0.jar!/" />
</CLASSES> </CLASSES>
<JAVADOC> <JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/com/google/guava/guava/17.0/guava-17.0-javadoc.jar!/" /> <root url="jar://$MAVEN_REPOSITORY$/com/google/guava/guava/18.0/guava-18.0-javadoc.jar!/" />
</JAVADOC> </JAVADOC>
<SOURCES> <SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/com/google/guava/guava/17.0/guava-17.0-sources.jar!/" /> <root url="jar://$MAVEN_REPOSITORY$/com/google/guava/guava/18.0/guava-18.0-sources.jar!/" />
</SOURCES> </SOURCES>
</library> </library>
</component> </component>
\ No newline at end of file
.idea/libraries/Maven__org_apache_commons_commons_pool2_2_2.xml deleted 100644 → 0
+ 0
− 13
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<component name="libraryTable">
<library name="Maven: org.apache.commons:commons-pool2:2.2">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-pool2/2.2/commons-pool2-2.2.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-pool2/2.2/commons-pool2-2.2-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-pool2/2.2/commons-pool2-2.2-sources.jar!/" />
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__org_broadinstitute_gatk_gatk_queue_package_distribution_3_3.xml 0 → 100644
+ 13
− 0
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<component name="libraryTable">
<library name="Maven: org.broadinstitute.gatk:gatk-queue-package-distribution:3.3">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/org/broadinstitute/gatk/gatk-queue-package-distribution/3.3/gatk-queue-package-distribution-3.3.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/org/broadinstitute/gatk/gatk-queue-package-distribution/3.3/gatk-queue-package-distribution-3.3-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/org/broadinstitute/gatk/gatk-queue-package-distribution/3.3/gatk-queue-package-distribution-3.3-sources.jar!/" />
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__redis_clients_jedis_2_5_1.xml deleted 100644 → 0
+ 0
− 13
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<component name="libraryTable">
<library name="Maven: redis.clients:jedis:2.5.1">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/redis/clients/jedis/2.5.1/jedis-2.5.1.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/redis/clients/jedis/2.5.1/jedis-2.5.1-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/redis/clients/jedis/2.5.1/jedis-2.5.1-sources.jar!/" />
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/misc.xml
+ 1
− 1
View file @ 25a8538c
...@@ -10,7 +10,7 @@ ...@@ -10,7 +10,7 @@
</list> </list>
</option> </option>
</component> </component>
<component name="ProjectRootManager" version="2" languageLevel="JDK_1_6" assert-keyword="true" jdk-15="true" project-jdk-name="1.8" project-jdk-type="JavaSDK"> <component name="ProjectRootManager" version="2" languageLevel="JDK_1_6" assert-keyword="true" jdk-15="true" project-jdk-name="1.7" project-jdk-type="JavaSDK">
<output url="file://$PROJECT_DIR$/out" /> <output url="file://$PROJECT_DIR$/out" />
</component> </component>
</project> </project>
......
biopet-framework/BiopetFramework.iml
+ 3
− 6
View file @ 25a8538c
...@@ -21,6 +21,7 @@ ...@@ -21,6 +21,7 @@
<sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" /> <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
<sourceFolder url="file://$MODULE_DIR$/src/test/scala" isTestSource="true" /> <sourceFolder url="file://$MODULE_DIR$/src/test/scala" isTestSource="true" />
<sourceFolder url="file://$MODULE_DIR$/src/main/scripts" type="java-resource" /> <sourceFolder url="file://$MODULE_DIR$/src/main/scripts" type="java-resource" />
<sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
<sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" /> <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
<excludeFolder url="file://$MODULE_DIR$/target" /> <excludeFolder url="file://$MODULE_DIR$/target" />
</content> </content>
...@@ -38,18 +39,14 @@ ...@@ -38,18 +39,14 @@
<orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" /> <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" />
<orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.11.2" level="project" /> <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.11.2" 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: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" />
<orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-package-distribution:3.2" level="project" /> <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-package-distribution:3.3" level="project" />
<orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" 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.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-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: 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-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: org.biojava:biojava3-sequencing:3.1.0" level="project" />
<orderEntry type="library" name="Maven: com.google.guava:guava:17.0" level="project" /> <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
<orderEntry type="library" name="Maven: com.baqend:bloom-filter:1.02" level="project" />
<orderEntry type="library" name="Maven: redis.clients:jedis:2.5.1" level="project" />
<orderEntry type="library" name="Maven: org.apache.commons:commons-pool2:2.2" level="project" />
<orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.4" level="project" />
<orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" /> <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" />
</component> </component>
</module> </module>
......
biopet-framework/pom.xml
+ 3
− 7
View file @ 25a8538c
...@@ -24,10 +24,6 @@ ...@@ -24,10 +24,6 @@
<name>BioJava repository</name> <name>BioJava repository</name>
<url>http://www.biojava.org/download/maven/</url> <url>http://www.biojava.org/download/maven/</url>
</repository> </repository>
<repository>
<id>orestes-bloom-filter</id>
<url>https://raw.githubusercontent.com/Baqend/Orestes-Bloomfilter/master/maven-repo</url>
</repository>
</repositories> </repositories>
<dependencies> <dependencies>
<dependency> <dependency>
...@@ -67,9 +63,9 @@ ...@@ -67,9 +63,9 @@
<version>3.1.0</version> <version>3.1.0</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>com.baqend</groupId> <groupId>com.google.guava</groupId>
<artifactId>bloom-filter</artifactId> <artifactId>guava</artifactId>
<version>1.02</version> <version>18.0</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>com.github.scopt</groupId> <groupId>com.github.scopt</groupId>
......
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