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Merge remote-tracking branch 'unstable/master'
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@eitanbanks
eitanbanks committed Jul 24, 2012
2 parents 91f02df + d067f97 commit b142977
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1,413 changes: 748 additions & 665 deletions build.xml
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168 changes: 86 additions & 82 deletions ivy.xml
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<ivy-module version="1.0">
<info organisation="org.broadinstitute" module="Sting"/>
<configurations defaultconfmapping="test->default">
<conf name="default" description="the core dependencies for the GATK"/>
<conf name="test" extends="default" description="external dependencies used for testing and metrics" />
<conf name="scala" extends="default" description="the dependencies for scala"/>
<conf name="queue" extends="scala" description="the dependencies for Queue"/>
</configurations>
<dependencies defaultconf="default">
<dependency org="net.sf" name="sam" rev="latest.integration"/>
<dependency org="net.sf" name="picard" rev="latest.integration"/>
<dependency org="edu.mit.broad" name="picard-private-parts" rev="latest.integration"/>

<!-- Tribble -->
<dependency org="org.broad" name="tribble" rev="latest.integration"/>

<dependency org="log4j" name="log4j" rev="1.2.15"/>
<dependency org="javax.mail" name="mail" rev="1.4.4"/>
<dependency org="colt" name="colt" rev="1.2.0"/>
<!-- <dependency org="jboss" name="javassist" rev="3.7.ga"/> -->
<dependency org="org.simpleframework" name="simple-xml" rev="2.0.4"/>
<dependency org="org.apache.bcel" name="bcel" rev="5.2"/>

<!-- Dependencies for reflections mvn repository -->
<dependency org="org.reflections" name="reflections" rev="0.9.5-RC2"/>

<!-- Matrix package from math.nist.gov -->
<dependency org="gov.nist" name="Jama" rev="1.0.2"/>

<!-- Dependencies for the graph aligner -->
<dependency org="org.jgrapht" name="jgrapht-jdk1.5" rev="0.7.3"/>

<!-- Dependencies for the html walker documention -->
<dependency org="org.freemarker" name="freemarker" rev="2.3.18"/>

<!-- Commons Dependencies -->
<dependency org="org.apache.commons" name="commons-email" rev="1.2"/>
<dependency org="org.apache.commons" name="commons-jexl" rev="2.0"/>
<dependency org="commons-lang" name="commons-lang" rev="2.5"/>
<dependency org="commons-logging" name="commons-logging" rev="1.1.1"/>
<dependency org="commons-io" name="commons-io" rev="2.1"/>
<dependency org="org.apache.commons" name="commons-math" rev="2.2" />

<!-- Lucene core utilities -->
<!-- <dependency org="org.apache.lucene" name="lucene-core" rev="3.0.3"/> -->

<!-- Dependencies for LSF, DRMAA, and other C libraries -->
<dependency org="net.java.dev.jna" name="jna" rev="3.2.7"/>

<!-- Dependencies for amazon.com S3 support -->
<dependency org="net.java.dev.jets3t" name="jets3t" rev="0.8.1"/>

<!-- Dependencies for GridEngine -->
<dependency org="net.sf.gridscheduler" name="drmaa" rev="latest.integration"/>

<!-- Scala dependancies -->
<dependency org="org.scala-lang" name="scala-compiler" rev="2.8.1"/>
<dependency org="org.scala-lang" name="scala-library" rev="2.8.1"/>

<!-- testing and evaluation dependencies -->
<dependency org="org.testng" name="testng" rev="5.14.1" conf="test" />
<dependency org="net.sourceforge.findbugs" name="findbugs" rev="1.3.2" conf="test"/>
<dependency org="net.sourceforge.findbugs" name="findbugs-ant" rev="1.3.2" conf="test"/>
<dependency org="net.sourceforge.findbugs" name="annotations" rev="1.3.2" conf="test"/>
<dependency org="net.sourceforge.findbugs" name="jsr305" rev="1.3.2" conf="test"/>
<dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT" conf="test" />

<!-- Contracts for Java and dependencies -->
<dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-20110609" />
<dependency org="asm" name="asm-all" rev="3.3.1" />

<!-- POI, for reading pipeline files -->
<dependency org="org.apache.poi" name="poi" rev="3.8-beta3" />
<dependency org="org.apache.poi" name="poi-ooxml" rev="3.8-beta3" />

<!-- snpEff annotator for pipelines -->
<dependency org="net.sf.snpeff" name="snpeff" rev="2.0.5" />

<!-- Exclude dependencies on sun libraries where the downloads aren't available but included in the jvm. -->
<exclude org="javax.servlet" />
<exclude org="javax.jms" />
<exclude org="com.sun.*" />
</dependencies>
<info organisation="org.broadinstitute" module="Sting"/>
<configurations defaultconfmapping="test->default">
<conf name="default" description="the core dependencies for the GATK"/>
<conf name="test" extends="default" description="external dependencies used for testing and metrics"/>
<conf name="scala" extends="default" description="the dependencies for scala"/>
<conf name="queue" extends="scala" description="the dependencies for Queue"/>
</configurations>
<dependencies defaultconf="default">
<dependency org="net.sf" name="sam" rev="latest.integration"/>
<dependency org="net.sf" name="picard" rev="latest.integration"/>
<dependency org="edu.mit.broad" name="picard-private-parts" rev="latest.integration"/>

<!-- Tribble -->
<dependency org="org.broad" name="tribble" rev="latest.integration"/>

<dependency org="log4j" name="log4j" rev="1.2.15"/>
<dependency org="javax.mail" name="mail" rev="1.4.4"/>
<dependency org="colt" name="colt" rev="1.2.0"/>
<!-- <dependency org="jboss" name="javassist" rev="3.7.ga"/> -->
<dependency org="org.simpleframework" name="simple-xml" rev="2.0.4"/>
<dependency org="org.apache.bcel" name="bcel" rev="5.2"/>

<!-- Dependencies for reflections mvn repository -->
<dependency org="org.reflections" name="reflections" rev="0.9.5-RC2"/>

<!-- Matrix package from math.nist.gov -->
<dependency org="gov.nist" name="Jama" rev="1.0.2"/>

<!-- Dependencies for the graph aligner -->
<dependency org="org.jgrapht" name="jgrapht-jdk1.5" rev="0.7.3"/>

<!-- Dependencies for the html walker documention -->
<dependency org="org.freemarker" name="freemarker" rev="2.3.18"/>

<!-- Commons Dependencies -->
<dependency org="org.apache.commons" name="commons-email" rev="1.2"/>
<dependency org="org.apache.commons" name="commons-jexl" rev="2.1.1"/>
<dependency org="commons-lang" name="commons-lang" rev="2.5"/>
<dependency org="commons-logging" name="commons-logging" rev="1.1.1"/>
<dependency org="commons-io" name="commons-io" rev="2.1"/>
<dependency org="org.apache.commons" name="commons-math" rev="2.2"/>

<!-- Lucene core utilities -->
<!-- <dependency org="org.apache.lucene" name="lucene-core" rev="3.0.3"/> -->

<!-- Dependencies for LSF, DRMAA, and other C libraries -->
<dependency org="net.java.dev.jna" name="jna" rev="3.2.7"/>

<!-- Dependencies for amazon.com S3 support -->
<dependency org="net.java.dev.jets3t" name="jets3t" rev="0.8.1"/>

<!-- Dependencies for GridEngine -->
<dependency org="net.sf.gridscheduler" name="drmaa" rev="latest.integration"/>

<!-- Scala dependancies -->
<dependency org="org.scala-lang" name="scala-compiler" rev="2.8.1"/>
<dependency org="org.scala-lang" name="scala-library" rev="2.8.1"/>

<!-- testing and evaluation dependencies -->
<dependency org="org.testng" name="testng" rev="5.14.1" conf="test"/>
<dependency org="org.uncommons" name="reportng" rev="1.1.2" conf="test"/>
<dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT" conf="test"/>

<!-- Contracts for Java and dependencies -->
<dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-20110609"/>
<dependency org="asm" name="asm-all" rev="3.3.1"/>

<!-- POI, for reading pipeline files -->
<dependency org="org.apache.poi" name="poi" rev="3.8-beta3"/>
<dependency org="org.apache.poi" name="poi-ooxml" rev="3.8-beta3"/>

<!-- snpEff annotator for pipelines -->
<dependency org="net.sf.snpeff" name="snpeff" rev="2.0.5"/>

<!-- MongoDB for the GXDB project -->
<dependency org="org.mongodb" name="mongo-java-driver" rev="2.7.3"/>

<!-- GSON and HTTP for talking to the REST API on Vanilla Forums -->
<dependency org="com.google.code.gson" name="gson" rev="2.2.2"/>
<dependency org="org.apache.httpcomponents" name="httpclient" rev="4.1.1"/>

<!-- Exclude dependencies on sun libraries where the downloads aren't available but included in the jvm. -->
<exclude org="javax.servlet"/>
<exclude org="javax.jms"/>
<exclude org="com.sun.*"/>
</dependencies>
</ivy-module>
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121 changes: 0 additions & 121 deletions .../R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_OtherCovariate.R
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84 changes: 0 additions & 84 deletions ...pts/org/broadinstitute/sting/analyzecovariates/plot_residualError_QualityScoreCovariate.R
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