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Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Matt Hanna 2011-07-17 20:59:12 -04:00
parent 28274187e2 00b650a35d
commit cda90f66fe
513 changed files with 5360 additions and 3894 deletions
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162
build.xml
View File

@ -28,6 +28,7 @@
<property name="build.dir" value="build" /> <property name="build.dir" value="build" />
<property name="dist.dir" value="dist" /> <property name="dist.dir" value="dist" />
<property name="lib.dir" value="lib" />
<property name="external.dir" value="external" /> <property name="external.dir" value="external" />
<property name="public.dir" value="public" /> <property name="public.dir" value="public" />
<property name="private.dir" value="private" /> <property name="private.dir" value="private" />
@ -44,11 +45,11 @@
<property name="queue-extensions.source.dir" value="${build.dir}/queue-extensions/src" /> <property name="queue-extensions.source.dir" value="${build.dir}/queue-extensions/src" />
<!-- Contracts for Java --> <!-- Contracts for Java -->
<!-- uncomment out to enable building contracts --> <!-- To disable, run with -Duse.contracts=false -->
<property name="use.contracts" value="true" /> <property name="use.contracts" value="true" />
<property name="java.contracts" value="${build.dir}/java/contracts" /> <property name="java.contracts" value="${build.dir}/java/contracts" />
<property name="cofojaDir" value="settings/repository/com.google/"/> <property name="contracts.version" value="1.0-20110609" />
<property name="cofoja.jar" value="${cofojaDir}/cofoja-1.0-20110609.jar"/> <property name="cofoja.jar" value="${lib.dir}/cofoja-${contracts.version}.jar"/>
<!-- where to find the tribble distro --> <!-- where to find the tribble distro -->
<property name="tribble.dir" value="tribble" /> <property name="tribble.dir" value="tribble" />
@ -69,8 +70,6 @@
<property environment="env"/> <property environment="env"/>
<property name="drmaa.jar" value="${env.SGE_ROOT}/lib/drmaa.jar" />
<patternset id="java.source.pattern"> <patternset id="java.source.pattern">
<include name="${java.public.source.dir}/**/*.java" /> <include name="${java.public.source.dir}/**/*.java" />
<include name="${java.private.source.dir}/**/*.java" if="include.private" /> <include name="${java.private.source.dir}/**/*.java" if="include.private" />
@ -103,7 +102,7 @@
</patternset> </patternset>
<path id="external.dependencies"> <path id="external.dependencies">
<fileset dir="lib"> <fileset dir="${lib.dir}">
<patternset refid="dependency.mask" /> <patternset refid="dependency.mask" />
</fileset> </fileset>
</path> </path>
@ -128,14 +127,14 @@
<!-- ivy properties --> <!-- ivy properties -->
<property name="ivy.install.version" value="2.2.0"/> <property name="ivy.install.version" value="2.2.0"/>
<property name="ivy.home" value="${user.home}/.ant"/> <property name="ivy.home" value="${user.home}/.ant"/>
<property name="ivy.jar.dir" value="${ivy.home}/lib"/> <property name="ivy.jar.dir" value="${ivy.home}/${lib.dir}"/>
<property name="ivy.jar.file" value="ivy-${ivy.install.version}.jar"/> <property name="ivy.jar.file" value="ivy-${ivy.install.version}.jar"/>
<property name="ivy.settings.dir" value="settings"/> <property name="ivy.settings.dir" value="settings"/>
<property file="${ivy.settings.dir}/ivysettings.properties"/> <property file="${ivy.settings.dir}/ivysettings.properties"/>
<mkdir dir="lib"/> <mkdir dir="${lib.dir}"/>
<mkdir dir="${ivy.jar.dir}"/> <mkdir dir="${ivy.jar.dir}"/>
<copy file="${cofoja.jar}" toFile="lib/cofoja.jar"/>
<get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}" <get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}"
dest="${ivy.jar.dir}/${ivy.jar.file}" dest="${ivy.jar.dir}/${ivy.jar.file}"
usetimestamp="true"/> usetimestamp="true"/>
@ -146,11 +145,7 @@
<property name="init.resolve.done" value="true"/> <property name="init.resolve.done" value="true"/>
</target> </target>
<target name="init.gridengine" depends="init" if="include.gridengine"> <target name="resolve" depends="init.resolve,init"
<copy todir="lib" file="${drmaa.jar}"/>
</target>
<target name="resolve" depends="init.resolve,init,init.gridengine"
description="locate and download library dependencies"> description="locate and download library dependencies">
<property name="ivy.conf" value="default"/> <property name="ivy.conf" value="default"/>
<ivy:retrieve file="ivy.xml" conf="${ivy.conf}" /> <ivy:retrieve file="ivy.xml" conf="${ivy.conf}" />
@ -178,13 +173,23 @@
<property name="build.version" value="${git.describe.output}" /> <property name="build.version" value="${git.describe.output}" />
</target> </target>
<target name="untagged.build.version" depends="git.describe" unless="git.describe.succeeded"> <target name="git.rev-parse" depends="git.describe" unless="git.describe.succeeded">
<exec executable="git" outputproperty="build.version" failonerror="true"> <exec executable="git" outputproperty="git.rev-parse.output" resultproperty="git.rev-parse.exit.value" failonerror="false">
<arg line="rev-parse HEAD" /> <arg line="rev-parse HEAD" />
</exec> </exec>
<condition property="git.rev-parse.succeeded">
<equals arg1="${git.rev-parse.exit.value}" arg2="0" />
</condition>
</target> </target>
<target name="generate.build.version" depends="tagged.build.version, untagged.build.version" /> <target name="untagged.build.version" depends="git.rev-parse" if="git.rev-parse.succeeded">
<property name="build.version" value="${git.rev-parse.output}" />
</target>
<target name="generate.build.version" depends="tagged.build.version, untagged.build.version">
<!-- Set build.version to exported if no other value has been set -->
<property name="build.version" value="exported" />
</target>
<!-- define some key locations that might change based on how the build is run --> <!-- define some key locations that might change based on how the build is run -->
<target name="init" depends="generate.build.version"> <target name="init" depends="generate.build.version">
@ -214,12 +219,6 @@
</or> </or>
</condition> </condition>
<!-- Include Grid Engine in the compile if SGE_ROOT is available. -->
<!-- Based off of http://wikis.sun.com/display/GridEngine/Automating+Grid+Engine+Functions+Through+DRMAA -->
<condition property="include.gridengine">
<available file="${drmaa.jar}"/>
</condition>
<echo message="GATK build : ${gatk.target}"/> <echo message="GATK build : ${gatk.target}"/>
<echo message="Scala build : ${scala.target}"/> <echo message="Scala build : ${scala.target}"/>
<echo message="source revision : ${build.version}"/> <echo message="source revision : ${build.version}"/>
@ -229,6 +228,10 @@
<equals arg1="${gatk.target}" arg2="private" casesensitive="false" /> <equals arg1="${gatk.target}" arg2="private" casesensitive="false" />
</condition> </condition>
<condition property="include.contracts">
<equals arg1="${use.contracts}" arg2="true" />
</condition>
<!-- Create the build directory structure used by compile --> <!-- Create the build directory structure used by compile -->
<mkdir dir="${build.dir}"/> <mkdir dir="${build.dir}"/>
<mkdir dir="${java.classes}"/> <mkdir dir="${java.classes}"/>
@ -252,7 +255,7 @@
<target name="init.scala.compile" depends="resolve" <target name="init.scala.compile" depends="resolve"
description="Initializes the scala ant tasks from scala-compiler.jar"> description="Initializes the scala ant tasks from scala-compiler.jar">
<path id="scala.classpath"> <path id="scala.classpath">
<fileset dir="lib"> <fileset dir="${lib.dir}">
<include name="scala-compiler-*.jar"/> <include name="scala-compiler-*.jar"/>
<include name="scala-library-*.jar"/> <include name="scala-library-*.jar"/>
</fileset> </fileset>
@ -287,7 +290,7 @@
depends="gatk.compile.public.source,gatk.compile.private.source,gatk.compile.external.source" depends="gatk.compile.public.source,gatk.compile.private.source,gatk.compile.external.source"
description="compile the GATK source" /> description="compile the GATK source" />
<target name="gatk.contracts.public" depends="gatk.compile.source"> <target name="gatk.contracts.public" depends="gatk.compile.source" if="include.contracts">
<javac fork="true" memoryMaximumSize="512m" srcdir="${java.public.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" > <javac fork="true" memoryMaximumSize="512m" srcdir="${java.public.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
<classpath> <classpath>
<path refid="external.dependencies" /> <path refid="external.dependencies" />
@ -299,7 +302,16 @@
</javac> </javac>
</target> </target>
<target name="gatk.contracts.private" depends="gatk.compile.source" if="include.private"> <target name="check.contracts.private" depends="gatk.contracts.public">
<condition property="include.contracts.private">
<and>
<isset property="include.contracts" />
<isset property="include.private" />
</and>
</condition>
</target>
<target name="gatk.contracts.private" depends="check.contracts.private" if="include.contracts.private">
<javac fork="true" memoryMaximumSize="512m" srcdir="${java.private.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" > <javac fork="true" memoryMaximumSize="512m" srcdir="${java.private.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
<classpath> <classpath>
<path refid="external.dependencies" /> <path refid="external.dependencies" />
@ -312,7 +324,7 @@
</target> </target>
<target name="gatk.contracts" depends="gatk.contracts.public,gatk.contracts.private" <target name="gatk.contracts" depends="gatk.contracts.public,gatk.contracts.private"
description="create GATK contracts" if="use.contracts" /> description="create GATK contracts" if="include.contracts" />
<target name="gatk.compile" depends="tribble,init,resolve,gatk.compile.source,gatk.contracts" /> <target name="gatk.compile" depends="tribble,init,resolve,gatk.compile.source,gatk.contracts" />
@ -357,7 +369,6 @@
<src path="${scala.public.source.dir}" /> <src path="${scala.public.source.dir}" />
<src path="${queue-extensions.source.dir}" /> <src path="${queue-extensions.source.dir}" />
<include name="**/*.scala"/> <include name="**/*.scala"/>
<exclude name="**/gridengine/**" unless="include.gridengine" />
</scalac> </scalac>
</target> </target>
@ -374,7 +385,6 @@
<scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.classes}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes"> <scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.classes}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
<src path="${scala.private.source.dir}" /> <src path="${scala.private.source.dir}" />
<include name="**/*.scala"/> <include name="**/*.scala"/>
<exclude name="**/gridengine/**" unless="include.gridengine" />
</scalac> </scalac>
</target> </target>
@ -452,7 +462,7 @@
<target name="init.jar" depends="sting.compile,extracthelp"> <target name="init.jar" depends="sting.compile,extracthelp">
<mkdir dir="${dist.dir}"/> <mkdir dir="${dist.dir}"/>
<copy todir="${dist.dir}"> <copy todir="${dist.dir}">
<fileset dir="lib" includes="*.jar"/> <fileset dir="${lib.dir}" includes="*.jar"/>
</copy> </copy>
</target> </target>
@ -464,7 +474,7 @@
<exclude name="**/utils/variantcontext/**/*.class"/> <exclude name="**/utils/variantcontext/**/*.class"/>
</fileset> </fileset>
<fileset dir="${java.classes}" includes="**/commandline/**/*.class"/> <fileset dir="${java.classes}" includes="**/commandline/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/datasources/**/*.class"/> <fileset dir="${java.classes}" includes="**/sting/pipeline/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/jna/**/*.class"/> <fileset dir="${java.classes}" includes="**/sting/jna/**/*.class"/>
<fileset dir="${java.classes}" includes="net/sf/picard/**/*.class"/> <fileset dir="${java.classes}" includes="net/sf/picard/**/*.class"/>
<fileset dir="${java.classes}" includes="net/sf/samtools/**/*.class"/> <fileset dir="${java.classes}" includes="net/sf/samtools/**/*.class"/>
@ -663,7 +673,7 @@
<path refid="external.dependencies" /> <path refid="external.dependencies" />
<pathelement location="${java.classes}"/> <pathelement location="${java.classes}"/>
<pathelement location="${java.contracts}"/> <pathelement location="${java.contracts}"/>
<pathelement location="lib/testng-5.14.1.jar"/> <pathelement location="${lib.dir}/testng-5.14.1.jar"/>
</classpath> </classpath>
<compilerarg value="-proc:none"/> <compilerarg value="-proc:none"/>
<!-- <!--
@ -682,12 +692,11 @@
<src path="${scala.public.test.sources}" /> <src path="${scala.public.test.sources}" />
<src path="${scala.private.test.sources}" /> <src path="${scala.private.test.sources}" />
<include name="**/*.scala"/> <include name="**/*.scala"/>
<exclude name="**/gridengine/**" unless="include.gridengine" />
<classpath> <classpath>
<path refid="scala.dependencies"/> <path refid="scala.dependencies"/>
<pathelement location="${scala.test.classes}"/> <pathelement location="${scala.test.classes}"/>
<pathelement location="${java.test.classes}"/> <pathelement location="${java.test.classes}"/>
<pathelement location="lib/testng-5.14.1.jar"/> <pathelement location="${lib.dir}/testng-5.14.1.jar"/>
</classpath> </classpath>
</scalac> </scalac>
</target> </target>
@ -727,9 +736,13 @@
<equals arg1="${pipeline.run}" arg2="$${pipeline.run}" /> <equals arg1="${pipeline.run}" arg2="$${pipeline.run}" />
</condition> </condition>
<condition property="cofoja.jvm.args" value="-javaagent:${cofoja.jar} -Dcom.google.java.contract.log.contract=false" else="">
<isset property="include.contracts" />
</condition>
<mkdir dir="${report}/@{testtype}"/> <mkdir dir="${report}/@{testtype}"/>
<echo message="Sting: Running @{testtype} test cases!"/> <echo message="Sting: Running @{testtype} test cases!"/>
<taskdef resource="testngtasks" classpath="lib/testng-5.14.1.jar"/> <taskdef resource="testngtasks" classpath="${lib.dir}/testng-5.14.1.jar"/>
<testng outputDir="${report}/@{testtype}" <testng outputDir="${report}/@{testtype}"
haltOnFailure="false" failureProperty="test.failure" haltOnFailure="false" failureProperty="test.failure"
verbose="2" verbose="2"
@ -740,9 +753,7 @@
<jvmarg value="-Djava.awt.headless=true" /> <jvmarg value="-Djava.awt.headless=true" />
<jvmarg value="-Dpipeline.run=${pipeline.run}" /> <jvmarg value="-Dpipeline.run=${pipeline.run}" />
<jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" /> <jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
<!-- needs to be if --> <jvmarg line="${cofoja.jvm.args}"/>
<!--jvmarg value="-javaagent:lib/cofoja.jar"/-->
<!--jvmarg value="-Dcom.google.java.contract.log.contract=false"/-->
<!-- <jvmarg value="-Xdebug"/> --> <!-- <jvmarg value="-Xdebug"/> -->
<!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> --> <!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
<classpath> <classpath>
@ -769,6 +780,50 @@
</sequential> </sequential>
</macrodef> </macrodef>
<!-- FAILED-TEST -->
<macrodef name="run-failed-test">
<attribute name="xmlfailedtestfile" />
<sequential>
<!-- Get the pipeline run type. Default to dry. -->
<condition property="pipeline.run" value="dry" else="${pipeline.run}">
<equals arg1="${pipeline.run}" arg2="$${pipeline.run}" />
</condition>
<condition property="cofoja.jvm.args" value="-javaagent:${cofoja.jar} -Dcom.google.java.contract.log.contract=false" else="">
<isset property="include.contracts" />
</condition>
<mkdir dir="${report}/failed_rerun" />
<echo message="Sting: Running @{xmlfailedtestfile} test cases!"/>
<taskdef resource="testngtasks" classpath="${lib.dir}/testng-5.14.1.jar"/>
<testng outputDir="${report}/failed_rerun"
haltOnFailure="false" failureProperty="test.failure"
verbose="2"
workingDir="${basedir}"
useDefaultListeners="false"
listeners="org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.sting.StingTextReporter">
<jvmarg value="-Xmx${test.maxmemory}" />
<jvmarg value="-Djava.awt.headless=true" />
<jvmarg value="-Dpipeline.run=${pipeline.run}" />
<jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
<jvmarg line="${cofoja.jvm.args}"/>
<!-- <jvmarg value="-Xdebug"/> -->
<!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
<classpath>
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />
<pathelement location="${scala.classes}" />
<pathelement location="${java.contracts}" />
<pathelement location="${java.test.classes}" />
<pathelement location="${scala.test.classes}" />
</classpath>
<xmlfileset dir="${basedir}" includes="@{xmlfailedtestfile}" />
</testng>
<fail message="test failed" if="test.failure" />
</sequential>
</macrodef>
<!-- our three different test conditions: Test, IntegrationTest, PerformanceTest --> <!-- our three different test conditions: Test, IntegrationTest, PerformanceTest -->
<target name="test" depends="test.compile,tribble.test" description="Run unit tests"> <target name="test" depends="test.compile,tribble.test" description="Run unit tests">
@ -803,6 +858,22 @@
<run-test testtype="${pipetype}"/> <run-test testtype="${pipetype}"/>
</target> </target>
<target name="failed-test" depends="test.compile">
<run-failed-test xmlfailedtestfile="${report}/*UnitTest/testng-failed.xml" />
</target>
<target name="failed-integration" depends="test.compile">
<run-failed-test xmlfailedtestfile="${report}/*IntegrationTest/testng-failed.xml" />
</target>
<target name="failed-performance" depends="test.compile">
<run-failed-test xmlfailedtestfile="${report}/*PerformanceTest/testng-failed.xml" />
</target>
<target name="failed-pipeline" depends="test.compile">
<run-failed-test xmlfailedtestfile="${report}/*PipelineTest/testng-failed.xml" />
</target>
<!-- ***************************************************************************** --> <!-- ***************************************************************************** -->
<!-- *********** Tribble ********* --> <!-- *********** Tribble ********* -->
<!-- ***************************************************************************** --> <!-- ***************************************************************************** -->
@ -820,7 +891,7 @@
<!-- copy the compiled library --> <!-- copy the compiled library -->
<target name="tribble.compile.copy" description="Copies the compiled tribble library" depends="tribble.compile" if="tribble.compile.exists"> <target name="tribble.compile.copy" description="Copies the compiled tribble library" depends="tribble.compile" if="tribble.compile.exists">
<copy todir="lib"> <copy todir="${lib.dir}">
<fileset dir="${tribble.dir}/dist" includes="*.jar"/> <fileset dir="${tribble.dir}/dist" includes="*.jar"/>
</copy> </copy>
</target> </target>
@ -828,7 +899,7 @@
<!-- copy the precompiled library --> <!-- copy the precompiled library -->
<target name="tribble.library.copy" description="Copies the precompiled tribble library" depends="tribble.init" unless="tribble.compile.exists"> <target name="tribble.library.copy" description="Copies the precompiled tribble library" depends="tribble.init" unless="tribble.compile.exists">
<echo message="Copying the Tribble Library..."/> <echo message="Copying the Tribble Library..."/>
<copy todir="lib"> <copy todir="${lib.dir}">
<fileset dir="settings/repository/org.broad" includes="tribble*.jar"/> <fileset dir="settings/repository/org.broad" includes="tribble*.jar"/>
</copy> </copy>
</target> </target>
@ -921,8 +992,8 @@
<pathconvert property="required.picard.jars" pathsep=":"> <pathconvert property="required.picard.jars" pathsep=":">
<fileset dir="${basedir}"> <fileset dir="${basedir}">
<include name="staging" /> <include name="staging" />
<include name="lib/picard-*.*.*.jar" /> <include name="${lib.dir}/picard-*.*.*.jar" />
<include name="lib/sam-*.jar" /> <include name="${lib.dir}/sam-*.jar" />
</fileset> </fileset>
</pathconvert> </pathconvert>
<echo message="required.picard.jars=${required.picard.jars}" /> <echo message="required.picard.jars=${required.picard.jars}" />
@ -944,7 +1015,7 @@
<!-- Find bug tasks --> <!-- Find bug tasks -->
<!-- ******************************************************************************** --> <!-- ******************************************************************************** -->
<path id="findbugs.classpath"> <path id="findbugs.classpath">
<fileset dir="lib" erroronmissingdir="true" includes="*.jar"/> <fileset dir="${lib.dir}" erroronmissingdir="true" includes="*.jar"/>
</path> </path>
<target name="findbugs" depends="dist"> <target name="findbugs" depends="dist">
<antcall target ="resolve"> <antcall target ="resolve">
@ -969,7 +1040,8 @@
<target name="clean" description="clean up" depends="tribble.clean,clean.javadoc"> <target name="clean" description="clean up" depends="tribble.clean,clean.javadoc">
<delete dir="out"/> <delete dir="out"/>
<delete dir="${build.dir}"/> <delete dir="${build.dir}"/>
<delete dir="lib"/> <delete dir="${lib.dir}"/>
<delete dir="dump"/>
<delete dir="staging"/> <delete dir="staging"/>
<delete dir="${dist.dir}"/> <delete dir="${dist.dir}"/>
<delete dir="pipelinetests"/> <delete dir="pipelinetests"/>

7
ivy.xml
View File

@ -48,6 +48,9 @@
<!-- Dependencies for amazon.com S3 support --> <!-- Dependencies for amazon.com S3 support -->
<dependency org="net.java.dev.jets3t" name="jets3t" rev="0.8.0"/> <dependency org="net.java.dev.jets3t" name="jets3t" rev="0.8.0"/>
<!-- Dependencies for GridEngine -->
<dependency org="net.sf.gridscheduler" name="drmaa" rev="latest.integration"/>
<!-- Scala dependancies --> <!-- Scala dependancies -->
<dependency org="org.scala-lang" name="scala-compiler" rev="2.8.1"/> <dependency org="org.scala-lang" name="scala-compiler" rev="2.8.1"/>
<dependency org="org.scala-lang" name="scala-library" rev="2.8.1"/> <dependency org="org.scala-lang" name="scala-library" rev="2.8.1"/>
@ -60,6 +63,10 @@
<dependency org="net.sourceforge.findbugs" name="jsr305" 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" /> <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 --> <!-- POI, for reading pipeline files -->
<dependency org="org.apache.poi" name="poi" rev="3.8-beta3" /> <dependency org="org.apache.poi" name="poi" rev="3.8-beta3" />
<dependency org="org.apache.poi" name="poi-ooxml" rev="3.8-beta3" /> <dependency org="org.apache.poi" name="poi-ooxml" rev="3.8-beta3" />

190
public/R/plot_Annotations_BinnedTruthMetrics.R
View File

@ -1,190 +0,0 @@
#!/bin/env Rscript
args <- commandArgs(TRUE)
verbose = TRUE
input = args[1]
annotationName = args[2]
minBinCutoff = as.numeric(args[3])
medianNumVariants = args[4]
c <- read.table(input, header=T)
all = c[c$numVariants>minBinCutoff & c$category=="all",]
novel = c[c$numVariants>minBinCutoff & c$category=="novel",]
dbsnp = c[c$numVariants>minBinCutoff & c$category=="dbsnp",]
truth = c[c$numVariants>minBinCutoff & c$category=="truth",]
#
# Calculate min, max, medians
#
d = c[c$numVariants>minBinCutoff,]
ymin = min(d$titv)
ymax = max(d$titv)
xmin = min(d$value)
xmax = max(d$value)
m = weighted.mean(all$value,all$numVariants/sum(all$numVariants))
ma = all[all$value > m,]
mb = all[all$value < m,]
m75 = weighted.mean(ma$value,ma$numVariants/sum(ma$numVariants))
m25 = weighted.mean(mb$value,mb$numVariants/sum(mb$numVariants))
if(medianNumVariants == "true") {
vc = cumsum( all$numVariants/sum(all$numVariants) )
m10 = all$value[ max(which(vc<=0.10)) ]
m25 = all$value[ max(which(vc<=0.25)) ]
m = all$value[ max(which(vc<=0.5)) ]
m75 = all$value[ min(which(vc>=0.75)) ]
m90 = all$value[ min(which(vc>=0.90)) ]
}
#
# Plot TiTv ratio as a function of the annotation
#
outfile = paste(input, ".TiTv.pdf", sep="")
pdf(outfile, height=7, width=7)
par(cex=1.1)
plot(all$value,all$titv,xlab=annotationName,ylab="Ti/Tv Ratio",pch=20,ylim=c(ymin,ymax),xaxt="n",ps=14);
axis(1,axTicks(1), format(axTicks(1), scientific=F))
abline(v=m,lty=2,col="red")
abline(v=m75,lty=3)
abline(v=m25,lty=3)
text(m, ymin, "50", col="red", cex=0.6);
text(m75, ymin, "75", col="black", cex=0.6);
text(m25, ymin, "25", col="black", cex=0.6);
if(medianNumVariants == "true") {
abline(v=m90,lty=3)
abline(v=m10,lty=3)
text(m10, ymin, "10", col="black", cex=0.6);
text(m90, ymin, "90", col="black", cex=0.6);
}
points(novel$value,novel$titv,col="green",pch=20)
points(dbsnp$value,dbsnp$titv,col="blue",pch=20)
if( sum(all$truePositive==0) != length(all$truePositive) ) {
points(truth$value,truth$titv,col="magenta",pch=20)
legend("topleft", c("all","novel","dbsnp","truth"),col=c("black","green","blue","magenta"),pch=c(20,20,20,20))
} else {
legend("topleft", c("all","novel","dbsnp"),col=c("black","green","blue"),pch=c(20,20,20))
}
dev.off()
#
# Plot TiTv ratio as a function of the annotation, log scale on the x-axis
#
outfile = paste(input, ".TiTv_log.pdf", sep="")
pdf(outfile, height=7, width=7)
par(cex=1.1)
plot(all$value,all$titv,xlab=annotationName,log="x",ylab="Ti/Tv Ratio",pch=20,ylim=c(ymin,ymax),xaxt="n",ps=14);
axis(1,axTicks(1), format(axTicks(1), scientific=F))
abline(v=m,lty=2,col="red")
abline(v=m75,lty=3)
abline(v=m25,lty=3)
text(m, ymin, "50", col="red", cex=0.6);
text(m75, ymin, "75", col="black", cex=0.6);
text(m25, ymin, "25", col="black", cex=0.6);
if(medianNumVariants == "true") {
abline(v=m90,lty=3)
abline(v=m10,lty=3)
text(m10, ymin, "10", col="black", cex=0.6);
text(m90, ymin, "90", col="black", cex=0.6);
}
points(novel$value,novel$titv,col="green",pch=20)
points(dbsnp$value,dbsnp$titv,col="blue",pch=20)
if( sum(all$truePositive==0) != length(all$truePositive) ) {
points(truth$value,truth$titv,col="magenta",pch=20)
legend("topleft", c("all","novel","dbsnp","truth"),col=c("black","green","blue","magenta"),pch=c(20,20,20,20))
} else {
legend("topleft", c("all","novel","dbsnp"),col=c("black","green","blue"),pch=c(20,20,20))
}
dev.off()
#
# Plot dbsnp and true positive rate as a function of the annotation
#
ymin = min(all$dbsnp)
ymax = max(all$dbsnp)
outfile = paste(input, ".truthRate.pdf", sep="")
pdf(outfile, height=7, width=7)
par(cex=1.1)
yLabel = "DBsnp Rate"
if( sum(all$truePositive==0) != length(all$truePositive) ) {
t = all[all$truePositive>0,]
yLabel = "DBsnp/True Positive Rate"
ymin = min(min(all$dbsnp),min(t$truePositive))
ymax = max(max(all$dbsnp),max(t$truePositive))
}
plot(all$value,all$dbsnp,xlab=annotationName,ylab=yLabel,pch=20,ylim=c(ymin,ymax),xaxt="n",ps=14);
axis(1,axTicks(1), format(axTicks(1), scientific=F))
abline(v=m,lty=2,col="red")
abline(v=m75,lty=3)
abline(v=m25,lty=3)
text(m, ymin, "50", col="red", cex=0.6);
text(m75, ymin, "75", col="black", cex=0.6);
text(m25, ymin, "25", col="black", cex=0.6);
if(medianNumVariants == "true") {
abline(v=m90,lty=3)
abline(v=m10,lty=3)
text(m10, ymin, "10", col="black", cex=0.6);
text(m90, ymin, "90", col="black", cex=0.6);
}
if( sum(all$truePositive==0) != length(all$truePositive) ) {
points(t$value,t$truePositive,col="magenta",pch=20);
legend("topleft", c("dbsnp","truth"),col=c("black","magenta"),pch=c(20,20))
}
dev.off()
#
# Plot dbsnp and true positive rate as a function of the annotation, log scale on the x-axis
#
outfile = paste(input, ".truthRate_log.pdf", sep="")
pdf(outfile, height=7, width=7)
par(cex=1.1)
yLabel = "DBsnp Rate"
if( sum(all$truePositive==0) != length(all$truePositive) ) {
yLabel = "DBsnp/Truth Rate"
}
plot(all$value,all$dbsnp,xlab=annotationName,log="x",ylab=yLabel,ylim=c(ymin,ymax),pch=20,xaxt="n",ps=14);
axis(1,axTicks(1), format(axTicks(1), scientific=F))
abline(v=m,lty=2,col="red")
abline(v=m75,lty=3)
abline(v=m25,lty=3)
text(m, ymin, "50", col="red", cex=0.6);
text(m75, ymin, "75", col="black", cex=0.6);
text(m25, ymin, "25", col="black", cex=0.6);
if(medianNumVariants == "true") {
abline(v=m90,lty=3)
abline(v=m10,lty=3)
text(m10, ymin, "10", col="black", cex=0.6);
text(m90, ymin, "90", col="black", cex=0.6);
}
if( sum(all$truePositive==0) != length(all$truePositive) ) {
points(t$value,t$truePositive,col="magenta",pch=20);
legend("topleft", c("dbsnp","truth"),col=c("black","magenta"),pch=c(20,20))
}
dev.off()
#
# Plot histogram of the annotation's value
#
outfile = paste(input, ".Histogram.pdf", sep="")
pdf(outfile, height=7, width=7)
par(cex=1.1)
plot(all$value,all$numVariants,xlab=annotationName,ylab="Num variants in bin",type="h",xaxt="n",ps=14,lwd=4);
axis(1,axTicks(1), format(axTicks(1), scientific=F))
dev.off()
#
# Plot histogram of the annotation's value, log scale on x-axis
#
outfile = paste(input, ".Histogram_log.pdf", sep="")
pdf(outfile, height=7, width=7)
par(cex=1.1)
plot(all$value,all$numVariants,xlab=annotationName,log="x",ylab="Num variants in bin",type="h",xaxt="n",ps=14,lwd=4);
axis(1,axTicks(1), format(axTicks(1), scientific=F))
dev.off()

13
public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
View File

@ -25,20 +25,21 @@
package org.broadinstitute.sting.analyzecovariates; package org.broadinstitute.sting.analyzecovariates;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.gatk.walkers.recalibration.*; import org.broadinstitute.sting.gatk.walkers.recalibration.Covariate;
import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum;
import org.broadinstitute.sting.gatk.walkers.recalibration.RecalibrationArgumentCollection;
import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import org.broadinstitute.sting.utils.text.XReadLines; import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.commandline.Argument;
import java.io.*;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collection; import java.util.Collection;
import java.util.List;
import java.util.Map; import java.util.Map;
import java.util.regex.Pattern; import java.util.regex.Pattern;
import java.io.*;
/** /**
* Created by IntelliJ IDEA. * Created by IntelliJ IDEA.
@ -61,7 +62,7 @@ public class AnalyzeCovariates extends CommandLineProgram {
@Argument(fullName = "path_to_Rscript", shortName = "Rscript", doc = "The path to your implementation of Rscript. For Broad users this is maybe /broad/tools/apps/R-2.6.0/bin/Rscript", required = false) @Argument(fullName = "path_to_Rscript", shortName = "Rscript", doc = "The path to your implementation of Rscript. For Broad users this is maybe /broad/tools/apps/R-2.6.0/bin/Rscript", required = false)
private String PATH_TO_RSCRIPT = "Rscript"; private String PATH_TO_RSCRIPT = "Rscript";
@Argument(fullName = "path_to_resources", shortName = "resources", doc = "Path to resources folder holding the Sting R scripts.", required = false) @Argument(fullName = "path_to_resources", shortName = "resources", doc = "Path to resources folder holding the Sting R scripts.", required = false)
private String PATH_TO_RESOURCES = "R/"; private String PATH_TO_RESOURCES = "public/R/";
@Argument(fullName = "ignoreQ", shortName = "ignoreQ", doc = "Ignore bases with reported quality less than this number.", required = false) @Argument(fullName = "ignoreQ", shortName = "ignoreQ", doc = "Ignore bases with reported quality less than this number.", required = false)
private int IGNORE_QSCORES_LESS_THAN = 5; private int IGNORE_QSCORES_LESS_THAN = 5;
@Argument(fullName = "numRG", shortName = "numRG", doc = "Only process N read groups. Default value: -1 (process all read groups)", required = false) @Argument(fullName = "numRG", shortName = "numRG", doc = "Only process N read groups. Default value: -1 (process all read groups)", required = false)

7
public/java/src/org/broadinstitute/sting/commandline/Argument.java
View File

@ -25,12 +25,7 @@
package org.broadinstitute.sting.commandline; package org.broadinstitute.sting.commandline;
import java.lang.annotation.Documented; import java.lang.annotation.*;
import java.lang.annotation.ElementType;
import java.lang.annotation.Inherited;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
import java.lang.annotation.Target;
/** /**
* Created by IntelliJ IDEA. * Created by IntelliJ IDEA.

4
public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java
View File

@ -27,10 +27,10 @@ package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.List;
import java.util.Collections;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator; import java.util.Iterator;
import java.util.List;
/** /**
* A group of argument definitions. * A group of argument definitions.

4
public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
View File

@ -27,10 +27,10 @@ package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.Set;
import java.util.HashSet;
import java.util.Collection; import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator; import java.util.Iterator;
import java.util.Set;
/** /**
* A collection of argument definitions. * A collection of argument definitions.

6
public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
View File

@ -25,12 +25,12 @@
package org.broadinstitute.sting.commandline; package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.gatk.walkers.Multiplex; import org.broadinstitute.sting.gatk.walkers.Multiplex;
import org.broadinstitute.sting.gatk.walkers.Multiplexer; import org.broadinstitute.sting.gatk.walkers.Multiplexer;
import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import java.lang.annotation.Annotation; import java.lang.annotation.Annotation;

10
public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
View File

@ -25,14 +25,20 @@
package org.broadinstitute.sting.commandline; package org.broadinstitute.sting.commandline;
import org.apache.log4j.*; import org.apache.log4j.FileAppender;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.PatternLayout;
import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.ApplicationDetails; import org.broadinstitute.sting.utils.help.ApplicationDetails;
import org.broadinstitute.sting.utils.help.HelpFormatter; import org.broadinstitute.sting.utils.help.HelpFormatter;
import java.io.IOException; import java.io.IOException;
import java.util.*; import java.util.Collection;
import java.util.Collections;
import java.util.EnumSet;
import java.util.Locale;
public abstract class CommandLineProgram { public abstract class CommandLineProgram {

10
public/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java
View File

@ -25,11 +25,17 @@
package org.broadinstitute.sting.commandline; package org.broadinstitute.sting.commandline;
import org.apache.log4j.*; import org.apache.log4j.Appender;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.Logger;
import org.apache.log4j.PatternLayout;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.*;
import java.lang.annotation.Annotation; import java.lang.annotation.Annotation;
import java.util.Collections;
import java.util.Enumeration;
import java.util.LinkedHashMap;
import java.util.Map;
/** /**
* Static utility methods for working with command-line arguments. * Static utility methods for working with command-line arguments.

2
public/java/src/org/broadinstitute/sting/commandline/MissingArgumentValueException.java
View File

@ -26,8 +26,6 @@ package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import java.util.Collection;
/** /**
* Specifies that a value was missing when attempting to populate an argument. * Specifies that a value was missing when attempting to populate an argument.
*/ */

10
public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
View File

@ -25,16 +25,16 @@
package org.broadinstitute.sting.commandline; package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.ApplicationDetails; import org.broadinstitute.sting.utils.help.ApplicationDetails;
import org.broadinstitute.sting.utils.help.HelpFormatter; import org.broadinstitute.sting.utils.help.HelpFormatter;
import org.apache.log4j.Logger;
import java.lang.reflect.*; import java.lang.reflect.Field;
import java.util.*; import java.util.*;
/** /**

4
public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java
View File

@ -27,10 +27,8 @@ package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import java.util.regex.Pattern;
import java.util.regex.Matcher; import java.util.regex.Matcher;
import java.util.List; import java.util.regex.Pattern;
import java.util.ArrayList;
/** /**
* Holds a pattern, along with how to get to the argument definitions that could match that pattern. * Holds a pattern, along with how to get to the argument definitions that could match that pattern.

21
public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
View File

@ -25,30 +25,21 @@
package org.broadinstitute.sting.gatk; package org.broadinstitute.sting.gatk;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor; import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.filters.ReadFilter; import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor; import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescriptor; import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor; import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor; import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport; import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.Walker;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.*;
import net.sf.picard.filter.SamRecordFilter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.text.ListFileUtils; import org.broadinstitute.sting.utils.text.ListFileUtils;
import org.broadinstitute.sting.utils.text.XReadLines;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
/** /**
* @author aaron * @author aaron

10
public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
View File

@ -26,13 +26,15 @@
package org.broadinstitute.sting.gatk; package org.broadinstitute.sting.gatk;
import org.broad.tribble.TribbleException; import org.broad.tribble.TribbleException;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.walkers.Attribution; import org.broadinstitute.sting.gatk.walkers.Attribution;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import org.broadinstitute.sting.utils.help.ApplicationDetails;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.ApplicationDetails;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import java.util.*; import java.util.*;

15
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
View File

@ -28,24 +28,14 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.picard.reference.ReferenceSequenceFile; import net.sf.picard.reference.ReferenceSequenceFile;
import net.sf.samtools.*; import net.sf.samtools.*;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.commandline.ArgumentException; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.commandline.ArgumentSource;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.commandline.CommandLineUtils;
import org.broadinstitute.sting.commandline.ParsingEngine;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; import org.broadinstitute.sting.gatk.datasources.reads.*;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource; import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.datasources.sample.Sample; import org.broadinstitute.sting.gatk.datasources.sample.Sample;
import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource; import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource;
import org.broadinstitute.sting.gatk.datasources.reads.MonolithicShardStrategy;
import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy;
import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategyFactory;
import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
import org.broadinstitute.sting.gatk.executive.MicroScheduler; import org.broadinstitute.sting.gatk.executive.MicroScheduler;
import org.broadinstitute.sting.gatk.filters.FilterManager; import org.broadinstitute.sting.gatk.filters.FilterManager;
import org.broadinstitute.sting.gatk.filters.ReadFilter; import org.broadinstitute.sting.gatk.filters.ReadFilter;
@ -65,6 +55,7 @@ import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.interval.IntervalUtils; import org.broadinstitute.sting.utils.interval.IntervalUtils;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.File; import java.io.File;
import java.util.*; import java.util.*;

9
public/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java
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@ -25,13 +25,12 @@
package org.broadinstitute.sting.gatk; package org.broadinstitute.sting.gatk;
import net.sf.picard.filter.SamRecordFilter; import net.sf.picard.filter.SamRecordFilter;
import java.util.Map;
import java.util.HashMap;
import java.util.Collections;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.Collections;
import java.util.HashMap;
import java.util.Map;
/** /**
* Holds a bunch of basic information about the traversal. * Holds a bunch of basic information about the traversal.
*/ */

1
public/java/src/org/broadinstitute/sting/gatk/ReadProperties.java
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@ -1,6 +1,5 @@
package org.broadinstitute.sting.gatk; package org.broadinstitute.sting.gatk;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileReader; import net.sf.samtools.SAMFileReader;

7
public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
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@ -25,19 +25,18 @@
package org.broadinstitute.sting.gatk; package org.broadinstitute.sting.gatk;
import net.sf.picard.filter.SamRecordFilter;
import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.commandline.Hidden;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.filters.FilterManager; import org.broadinstitute.sting.gatk.filters.FilterManager;
import org.broadinstitute.sting.gatk.filters.ReadFilter; import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.text.TextFormattingUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.DescriptionTaglet; import org.broadinstitute.sting.utils.help.DescriptionTaglet;
import org.broadinstitute.sting.utils.help.DisplayNameTaglet; import org.broadinstitute.sting.utils.help.DisplayNameTaglet;
import org.broadinstitute.sting.utils.help.SummaryTaglet; import org.broadinstitute.sting.utils.help.SummaryTaglet;
import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import java.util.*; import java.util.*;

11
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -26,17 +26,16 @@
package org.broadinstitute.sting.gatk.arguments; package org.broadinstitute.sting.gatk.arguments;
import net.sf.samtools.SAMFileReader; import net.sf.samtools.SAMFileReader;
import org.broadinstitute.sting.commandline.Hidden;
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Hidden;
import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.gatk.DownsampleType; import org.broadinstitute.sting.gatk.DownsampleType;
import org.broadinstitute.sting.gatk.DownsamplingMethod; import org.broadinstitute.sting.gatk.DownsamplingMethod;
import org.broadinstitute.sting.utils.interval.IntervalSetRule; import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
import org.broadinstitute.sting.utils.interval.IntervalSetRule;
import org.simpleframework.xml.*; import org.simpleframework.xml.*;
import org.simpleframework.xml.core.Persister; import org.simpleframework.xml.core.Persister;
import org.simpleframework.xml.stream.Format; import org.simpleframework.xml.stream.Format;

6
public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
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@ -26,13 +26,13 @@
package org.broadinstitute.sting.gatk.contexts; package org.broadinstitute.sting.gatk.contexts;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.HasGenomeLocation; import org.broadinstitute.sting.utils.HasGenomeLocation;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.util.*; import java.util.List;
/** /**
* Useful class for forwarding on locusContext data from this iterator * Useful class for forwarding on locusContext data from this iterator

2
public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java
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@ -27,8 +27,8 @@ package org.broadinstitute.sting.gatk.contexts;
import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.gatk.datasources.sample.Sample; import org.broadinstitute.sting.gatk.datasources.sample.Sample;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.*; import org.broadinstitute.sting.utils.pileup.*;

9
public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
View File

@ -25,11 +25,12 @@
package org.broadinstitute.sting.gatk.contexts; package org.broadinstitute.sting.gatk.contexts;
import org.broadinstitute.sting.utils.GenomeLocParser; import com.google.java.contract.Ensures;
import org.broadinstitute.sting.utils.GenomeLoc; import com.google.java.contract.Requires;
import org.broadinstitute.sting.utils.BaseUtils;
import net.sf.samtools.util.StringUtil; import net.sf.samtools.util.StringUtil;
import com.google.java.contract.*; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
/** /**
* The section of the reference that overlaps with the given * The section of the reference that overlaps with the given

16
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java
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@ -1,16 +1,14 @@
package org.broadinstitute.sting.gatk.datasources.providers; package org.broadinstitute.sting.gatk.datasources.providers;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
import java.util.Collections;
import java.util.List; import java.util.List;
import java.util.NoSuchElementException; import java.util.NoSuchElementException;
import java.util.ArrayList;
import java.util.Collections;
import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.utils.GenomeLoc;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
/** /**
* User: hanna * User: hanna
* Date: May 13, 2009 * Date: May 13, 2009

11
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
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@ -1,13 +1,12 @@
package org.broadinstitute.sting.gatk.datasources.providers; package org.broadinstitute.sting.gatk.datasources.providers;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import net.sf.picard.reference.ReferenceSequence;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import net.sf.picard.reference.ReferenceSequence;
/* /*
* Copyright (c) 2009 The Broad Institute * Copyright (c) 2009 The Broad Institute
* *

9
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java
View File

@ -1,16 +1,15 @@
package org.broadinstitute.sting.gatk.datasources.providers; package org.broadinstitute.sting.gatk.datasources.providers;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.iterators.LocusIterator; import org.broadinstitute.sting.gatk.iterators.LocusIterator;
import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.Collection; import java.util.Collection;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.GenomeLocParser;
/** /**
* Presents data sharded by locus to the traversal engine. * Presents data sharded by locus to the traversal engine.
* *

2
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
View File

@ -1,7 +1,7 @@
package org.broadinstitute.sting.gatk.datasources.providers; package org.broadinstitute.sting.gatk.datasources.providers;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.DownsampleType; import org.broadinstitute.sting.gatk.DownsampleType;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.iterators.LocusIterator; import org.broadinstitute.sting.gatk.iterators.LocusIterator;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;

2
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
View File

@ -5,10 +5,10 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import java.util.List;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collection; import java.util.Collection;
import java.util.Collections; import java.util.Collections;
import java.util.List;
/** /**
* User: hanna * User: hanna
* Date: May 21, 2009 * Date: May 21, 2009

3
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java
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@ -1,9 +1,8 @@
package org.broadinstitute.sting.gatk.datasources.providers; package org.broadinstitute.sting.gatk.datasources.providers;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.GenomeLoc;
/* /*
* Copyright (c) 2009 The Broad Institute * Copyright (c) 2009 The Broad Institute
* *

7
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java
View File

@ -1,14 +1,13 @@
package org.broadinstitute.sting.gatk.datasources.providers; package org.broadinstitute.sting.gatk.datasources.providers;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.Collection; import java.util.Collection;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.GenomeLocParser;
/** /**
* Present data sharded by read to a traversal engine. * Present data sharded by read to a traversal engine.
* *

5
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java
View File

@ -1,11 +1,10 @@
package org.broadinstitute.sting.gatk.datasources.providers; package org.broadinstitute.sting.gatk.datasources.providers;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import java.util.Collection;
import java.util.Arrays; import java.util.Arrays;
import java.util.Collection;
import net.sf.samtools.SAMRecord;
/** /**
* User: hanna * User: hanna
* Date: May 22, 2009 * Date: May 22, 2009

18
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java
View File

@ -1,16 +1,16 @@
package org.broadinstitute.sting.gatk.datasources.providers; package org.broadinstitute.sting.gatk.datasources.providers;
import org.broadinstitute.sting.utils.*;
import java.util.Collections;
import java.util.Collection;
import java.util.Arrays;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.SAMRecord;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceRecord;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
/** /**
* User: hanna * User: hanna
* Date: May 22, 2009 * Date: May 22, 2009

4
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java
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@ -25,9 +25,9 @@
package org.broadinstitute.sting.gatk.datasources.providers; package org.broadinstitute.sting.gatk.datasources.providers;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;

5
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
View File

@ -1,15 +1,14 @@
package org.broadinstitute.sting.gatk.datasources.providers; package org.broadinstitute.sting.gatk.datasources.providers;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List;
import java.util.Collection; import java.util.Collection;
import java.util.List;
import net.sf.picard.reference.IndexedFastaSequenceFile;
/** /**
* User: hanna * User: hanna
* Date: May 8, 2009 * Date: May 8, 2009

5
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMBlockStartIterator.java
View File

@ -24,9 +24,6 @@
package org.broadinstitute.sting.gatk.datasources.reads; package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMRecord;
import org.apache.commons.lang.ArrayUtils;
import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.StingException;
import java.io.File; import java.io.File;
@ -35,9 +32,7 @@ import java.io.IOException;
import java.nio.ByteBuffer; import java.nio.ByteBuffer;
import java.nio.ByteOrder; import java.nio.ByteOrder;
import java.nio.channels.FileChannel; import java.nio.channels.FileChannel;
import java.util.ArrayList;
import java.util.Iterator; import java.util.Iterator;
import java.util.List;
/** /**
* Created by IntelliJ IDEA. * Created by IntelliJ IDEA.

7
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java
View File

@ -39,12 +39,7 @@ import java.io.RandomAccessFile;
import java.nio.ByteBuffer; import java.nio.ByteBuffer;
import java.nio.ByteOrder; import java.nio.ByteOrder;
import java.nio.channels.FileChannel; import java.nio.channels.FileChannel;
import java.util.ArrayList; import java.util.*;
import java.util.BitSet;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
/** /**
* Writes schedules for a single BAM file to a target output file. * Writes schedules for a single BAM file to a target output file.

12
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
View File

@ -26,20 +26,10 @@ package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.picard.util.PeekableIterator; import net.sf.picard.util.PeekableIterator;
import net.sf.samtools.GATKBAMFileSpan; import net.sf.samtools.GATKBAMFileSpan;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import java.io.File; import java.util.*;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.NoSuchElementException;
/** /**
* Assign intervals to the most appropriate blocks, keeping as little as possible in memory at once. * Assign intervals to the most appropriate blocks, keeping as little as possible in memory at once.

10
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java
View File

@ -29,19 +29,11 @@ import net.sf.samtools.GATKBAMFileSpan;
import net.sf.samtools.SAMFileSpan; import net.sf.samtools.SAMFileSpan;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
import org.broadinstitute.sting.utils.interval.IntervalUtils; import org.broadinstitute.sting.utils.interval.IntervalUtils;
import java.util.ArrayList; import java.util.*;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.SortedMap;
import java.util.TreeMap;
/** /**
* Represents a small section of a BAM file, and every associated interval. * Represents a small section of a BAM file, and every associated interval.

14
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
View File

@ -23,24 +23,18 @@
*/ */
package org.broadinstitute.sting.gatk.datasources.reads; package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.samtools.Bin; import net.sf.samtools.*;
import net.sf.samtools.GATKBAMFileSpan;
import net.sf.samtools.GATKBin;
import net.sf.samtools.GATKChunk;
import net.sf.samtools.LinearIndex;
import net.sf.samtools.SAMException;
import net.sf.samtools.util.RuntimeIOException;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.File; import java.io.File;
import java.io.FileInputStream; import java.io.FileInputStream;
import java.io.IOException; import java.io.IOException;
import java.lang.ref.SoftReference;
import java.nio.ByteBuffer; import java.nio.ByteBuffer;
import java.nio.ByteOrder; import java.nio.ByteOrder;
import java.nio.channels.FileChannel; import java.nio.channels.FileChannel;
import java.util.*; import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
/** /**
* A basic interface for querying BAM indices. * A basic interface for querying BAM indices.

6
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java
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@ -24,11 +24,7 @@
package org.broadinstitute.sting.gatk.datasources.reads; package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.samtools.Bin; import net.sf.samtools.*;
import net.sf.samtools.GATKBAMFileSpan;
import net.sf.samtools.GATKBin;
import net.sf.samtools.GATKChunk;
import net.sf.samtools.LinearIndex;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collections; import java.util.Collections;

11
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java
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@ -35,16 +35,7 @@ import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.ArrayList; import java.util.*;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.NoSuchElementException;
import java.util.PriorityQueue;
import java.util.Queue;
/** /**
* Shard intervals based on position within the BAM file. * Shard intervals based on position within the BAM file.

3
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java
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@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.datasources.reads; package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.samtools.SAMFileSpan;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
@ -7,8 +8,6 @@ import org.broadinstitute.sting.utils.Utils;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
import net.sf.samtools.SAMFileSpan;
/** /**
* Handles locus shards of BAM information. * Handles locus shards of BAM information.
* @author aaron * @author aaron

17
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardStrategy.java
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@ -24,17 +24,18 @@
package org.broadinstitute.sting.gatk.datasources.reads; package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.samtools.GATKBAMFileSpan; import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.GenomeLocSortedSet; import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileSpan;
import net.sf.samtools.SAMSequenceRecord;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import java.util.*; import java.util.ArrayList;
import java.util.Iterator;
import net.sf.samtools.SAMFileHeader; import java.util.List;
import net.sf.samtools.SAMSequenceRecord; import java.util.Map;
import net.sf.samtools.SAMFileSpan;
import net.sf.picard.reference.IndexedFastaSequenceFile;
/** /**
* A sharding strategy for loci based on reading of the index. * A sharding strategy for loci based on reading of the index.

2
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShard.java
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@ -1,8 +1,8 @@
package org.broadinstitute.sting.gatk.datasources.reads; package org.broadinstitute.sting.gatk.datasources.reads;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.GenomeLoc;
import java.util.List; import java.util.List;

2
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShardStrategy.java
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@ -4,8 +4,8 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.Iterator; import java.util.Iterator;
import java.util.NoSuchElementException;
import java.util.List; import java.util.List;
import java.util.NoSuchElementException;
/** /**
* Create a giant shard representing all the data in the input BAM(s). * Create a giant shard representing all the data in the input BAM(s).

14
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java
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@ -1,15 +1,17 @@
package org.broadinstitute.sting.gatk.datasources.reads; package org.broadinstitute.sting.gatk.datasources.reads;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter;
import java.util.*;
import net.sf.samtools.SAMFileSpan; import net.sf.samtools.SAMFileSpan;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Map;
/** /**
* *
* User: aaron * User: aaron

5
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardStrategy.java
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@ -25,12 +25,11 @@
package org.broadinstitute.sting.gatk.datasources.reads; package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.samtools.SAMFileSpan; import net.sf.samtools.SAMFileSpan;
import java.util.*;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import java.util.*;
/** /**
* The sharding strategy for reads using a simple counting mechanism. Each read shard * The sharding strategy for reads using a simple counting mechanism. Each read shard
* has a specific number of reads (default to 10K) which is configured in the constructor. * has a specific number of reads (default to 10K) which is configured in the constructor.

14
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
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@ -24,21 +24,19 @@
package org.broadinstitute.sting.gatk.datasources.reads; package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.picard.sam.MergingSamRecordIterator;
import net.sf.picard.sam.SamFileHeaderMerger;
import net.sf.samtools.*; import net.sf.samtools.*;
import net.sf.samtools.util.CloseableIterator; import net.sf.samtools.util.CloseableIterator;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.picard.sam.SamFileHeaderMerger;
import net.sf.picard.sam.MergingSamRecordIterator;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.DownsamplingMethod; import org.broadinstitute.sting.gatk.DownsamplingMethod;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.iterators.*;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.ReadMetrics; import org.broadinstitute.sting.gatk.ReadMetrics;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator; import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.iterators.*;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.baq.BAQ;

8
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java
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@ -2,17 +2,13 @@ package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.samtools.SAMFileSpan; import net.sf.samtools.SAMFileSpan;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.gatk.ReadMetrics; import org.broadinstitute.sting.gatk.ReadMetrics;
import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.HasGenomeLocation; import org.broadinstitute.sting.utils.HasGenomeLocation;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.Serializable;
import java.util.Collections; import java.util.Collections;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;

4
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategyFactory.java
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@ -1,10 +1,10 @@
package org.broadinstitute.sting.gatk.datasources.reads; package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.samtools.SAMSequenceDictionary;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
/** /**
* *

8
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java
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@ -25,17 +25,17 @@
package org.broadinstitute.sting.gatk.datasources.reads.utilities; package org.broadinstitute.sting.gatk.datasources.reads.utilities;
import org.broadinstitute.sting.commandline.CommandLineProgram; import net.sf.samtools.BAMIndex;
import net.sf.samtools.SAMFileReader;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.instrumentation.Sizeof; import org.broadinstitute.sting.utils.instrumentation.Sizeof;
import java.io.File; import java.io.File;
import java.lang.reflect.Field; import java.lang.reflect.Field;
import java.util.Map;
import java.util.List; import java.util.List;
import java.util.Map;
import net.sf.samtools.*;
/** /**
* *

8
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java
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@ -24,12 +24,12 @@
package org.broadinstitute.sting.gatk.datasources.reads.utilities; package org.broadinstitute.sting.gatk.datasources.reads.utilities;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.commandline.Argument;
import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMFileReader; import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMFileWriterFactory; import net.sf.samtools.SAMFileWriterFactory;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import java.io.File; import java.io.File;

1
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java
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@ -24,7 +24,6 @@
package org.broadinstitute.sting.gatk.datasources.reads.utilities; package org.broadinstitute.sting.gatk.datasources.reads.utilities;
import net.sf.samtools.SAMFileReader;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.CommandLineProgram; import org.broadinstitute.sting.commandline.CommandLineProgram;

11
public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java
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@ -25,16 +25,15 @@
package org.broadinstitute.sting.gatk.datasources.reference; package org.broadinstitute.sting.gatk.datasources.reference;
import net.sf.picard.reference.ReferenceSequenceFileFactory;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import net.sf.picard.reference.FastaSequenceIndexBuilder;
import net.sf.picard.sam.CreateSequenceDictionary;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.picard.reference.FastaSequenceIndex; import net.sf.picard.reference.FastaSequenceIndex;
import net.sf.picard.reference.FastaSequenceIndexBuilder;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.picard.sam.CreateSequenceDictionary;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.file.FSLockWithShared; import org.broadinstitute.sting.utils.file.FSLockWithShared;
import org.broadinstitute.sting.utils.file.FileSystemInabilityToLockException; import org.broadinstitute.sting.utils.file.FileSystemInabilityToLockException;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import java.io.File; import java.io.File;

6
public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java
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@ -28,11 +28,7 @@ import net.sf.samtools.SAMSequenceDictionary;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.ArrayList; import java.util.*;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
/** /**
* A pool of open resources, all of which can create a closeable iterator. * A pool of open resources, all of which can create a closeable iterator.

5
public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java
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@ -3,11 +3,10 @@ package org.broadinstitute.sting.gatk.datasources.sample;
import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.yaml.snakeyaml.TypeDescription; import org.yaml.snakeyaml.TypeDescription;
import org.yaml.snakeyaml.Yaml; import org.yaml.snakeyaml.Yaml;
import org.yaml.snakeyaml.constructor.Constructor; import org.yaml.snakeyaml.constructor.Constructor;

17
public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java
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@ -1,15 +1,20 @@
package org.broadinstitute.sting.gatk.examples; package org.broadinstitute.sting.gatk.examples;
import net.sf.samtools.*; import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.contexts.*;
import org.broadinstitute.sting.utils.pileup.*;
import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.util.*;
import java.io.PrintStream; import java.io.PrintStream;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
/** /**
* Computes the coverage per sample. * Computes the coverage per sample.

4
public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java
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@ -25,6 +25,8 @@
package org.broadinstitute.sting.gatk.examples; package org.broadinstitute.sting.gatk.examples;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -32,8 +34,6 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidSNPGenotypePriors; import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidSNPGenotypePriors;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.io.PrintStream; import java.io.PrintStream;

12
public/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
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@ -25,18 +25,18 @@
package org.broadinstitute.sting.gatk.executive; package org.broadinstitute.sting.gatk.executive;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List;
import java.util.Iterator; import java.util.Iterator;
import java.util.List;
/** /**
* Manages the * Manages the
*/ */

18
public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
View File

@ -1,27 +1,27 @@
package org.broadinstitute.sting.gatk.executive; package org.broadinstitute.sting.gatk.executive;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy; import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.io.*; import org.broadinstitute.sting.gatk.io.OutputTracker;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor; import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor;
import java.util.Queue;
import java.util.LinkedList;
import java.util.Collection; import java.util.Collection;
import java.util.concurrent.Executors; import java.util.LinkedList;
import java.util.Queue;
import java.util.concurrent.ExecutorService; import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future; import java.util.concurrent.Future;
import java.util.concurrent.FutureTask; import java.util.concurrent.FutureTask;
import net.sf.picard.reference.IndexedFastaSequenceFile;
/** /**
* A microscheduler that schedules shards according to a tree-like structure. * A microscheduler that schedules shards according to a tree-like structure.
* Requires a special walker tagged with a 'TreeReducible' interface. * Requires a special walker tagged with a 'TreeReducible' interface.

11
public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
View File

@ -1,22 +1,21 @@
package org.broadinstitute.sting.gatk.executive; package org.broadinstitute.sting.gatk.executive;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider; import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider; import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy; import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.io.DirectOutputTracker; import org.broadinstitute.sting.gatk.io.DirectOutputTracker;
import org.broadinstitute.sting.gatk.io.OutputTracker; import org.broadinstitute.sting.gatk.io.OutputTracker;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.Walker;
import java.util.Collection; import java.util.Collection;
import net.sf.picard.reference.IndexedFastaSequenceFile;
/** A micro-scheduling manager for single-threaded execution of a traversal. */ /** A micro-scheduling manager for single-threaded execution of a traversal. */
public class LinearMicroScheduler extends MicroScheduler { public class LinearMicroScheduler extends MicroScheduler {

25
public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
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@ -25,26 +25,18 @@
package org.broadinstitute.sting.gatk.executive; package org.broadinstitute.sting.gatk.executive;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy; import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.io.OutputTracker;
import org.broadinstitute.sting.gatk.iterators.NullSAMIterator;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.gatk.traversals.*; import org.broadinstitute.sting.gatk.traversals.*;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.io.OutputTracker;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.gatk.iterators.NullSAMIterator;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.ReadMetrics;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.PrintStream;
import java.lang.management.ManagementFactory;
import java.util.*;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.threading.*; import org.broadinstitute.sting.utils.threading.*;
@ -52,6 +44,11 @@ import org.broadinstitute.sting.utils.threading.*;
import javax.management.JMException; import javax.management.JMException;
import javax.management.MBeanServer; import javax.management.MBeanServer;
import javax.management.ObjectName; import javax.management.ObjectName;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.PrintStream;
import java.lang.management.ManagementFactory;
import java.util.Collection;
/** /**

3
public/java/src/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java
View File

@ -1,10 +1,9 @@
package org.broadinstitute.sting.gatk.executive; package org.broadinstitute.sting.gatk.executive;
import org.broadinstitute.sting.gatk.io.storage.Storage; import org.broadinstitute.sting.gatk.io.storage.Storage;
import org.broadinstitute.sting.gatk.io.OutputTracker;
import java.util.Collection;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collection;
/** /**
* User: hanna * User: hanna

4
public/java/src/org/broadinstitute/sting/gatk/executive/ReduceTree.java
View File

@ -1,9 +1,9 @@
package org.broadinstitute.sting.gatk.executive; package org.broadinstitute.sting.gatk.executive;
import java.util.Queue;
import java.util.List;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.LinkedList; import java.util.LinkedList;
import java.util.List;
import java.util.Queue;
import java.util.concurrent.Future; import java.util.concurrent.Future;
/** /**
* User: hanna * User: hanna

6
public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
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@ -1,13 +1,13 @@
package org.broadinstitute.sting.gatk.executive; package org.broadinstitute.sting.gatk.executive;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider; import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker; import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.concurrent.Callable; import java.util.concurrent.Callable;

2
public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
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@ -4,8 +4,8 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.concurrent.Callable; import java.util.concurrent.Callable;
import java.util.concurrent.Future;
import java.util.concurrent.ExecutionException; import java.util.concurrent.ExecutionException;
import java.util.concurrent.Future;
/** /**
* User: hanna * User: hanna
* Date: Apr 29, 2009 * Date: Apr 29, 2009

19
public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
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@ -1,17 +1,20 @@
package org.broadinstitute.sting.gatk.executive; package org.broadinstitute.sting.gatk.executive;
import org.broadinstitute.sting.gatk.datasources.reads.Shard; import net.sf.picard.util.PeekableIterator;
import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.gatk.iterators.*;
import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import java.util.*; import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource;
import org.broadinstitute.sting.gatk.iterators.LocusIterator;
import net.sf.picard.util.PeekableIterator; import org.broadinstitute.sting.gatk.iterators.LocusIteratorByState;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.Iterator;
import java.util.List;
import java.util.NoSuchElementException;
/** /**
* Buffer shards of data which may or may not contain multiple loci into * Buffer shards of data which may or may not contain multiple loci into
* iterators of all data which cover an interval. Its existence is an homage * iterators of all data which cover an interval. Its existence is an homage

6
public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java
View File

@ -24,8 +24,10 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter; import net.sf.samtools.Cigar;
import net.sf.samtools.*; import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMRecord;
/** /**
* Filter out reads with wonky cigar strings. * Filter out reads with wonky cigar strings.

1
public/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java
View File

@ -24,7 +24,6 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
/** /**

13
public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java
View File

@ -23,17 +23,16 @@
*/ */
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.samtools.util.CloserUtil; import net.sf.picard.filter.SamRecordFilter;
import java.util.Iterator;
import java.util.NoSuchElementException;
import java.util.Collection;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.CloseableIterator; import net.sf.samtools.util.CloseableIterator;
import net.sf.picard.filter.SamRecordFilter; import net.sf.samtools.util.CloserUtil;
import org.broadinstitute.sting.gatk.ReadMetrics; import org.broadinstitute.sting.gatk.ReadMetrics;
import java.util.Collection;
import java.util.Iterator;
import java.util.NoSuchElementException;
/** /**
* Filtering Iterator which takes a filter and an iterator and iterates * Filtering Iterator which takes a filter and an iterator and iterates
* through only those records which are not rejected by the filter. * through only those records which are not rejected by the filter.

1
public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java
View File

@ -1,6 +1,5 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
/* /*

1
public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckReadFilter.java
View File

@ -24,7 +24,6 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
/** /**

3
public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java
View File

@ -25,11 +25,8 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.classloader.PluginManager;
import net.sf.picard.filter.SamRecordFilter;
import java.util.Collection; import java.util.Collection;
/** /**

2
public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
View File

@ -24,8 +24,8 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceRecord; import net.sf.samtools.SAMSequenceRecord;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;

1
public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java
View File

@ -25,7 +25,6 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;

36
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java → public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java 100755 → 100644
View File

@ -1,6 +1,5 @@
/* /*
* Copyright (c) 2010, The Broad Institute * Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person * Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation * obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without * files (the "Software"), to deal in the Software without
@ -12,6 +11,7 @@
* *
* The above copyright notice and this permission notice shall be * The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software. * included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
@ -22,25 +22,21 @@
* OTHER DEALINGS IN THE SOFTWARE. * OTHER DEALINGS IN THE SOFTWARE.
*/ */
package org.broadinstitute.sting.gatk.walkers.variantutils; package org.broadinstitute.sting.gatk.filters;
import org.broadinstitute.sting.WalkerTest; import net.sf.samtools.SAMRecord;
import org.testng.annotations.Test; import org.broadinstitute.sting.utils.QualityUtils;
import java.io.File; /**
import java.util.Arrays; * Filter out mapping quality zero reads.
*
* @author ebanks
* @version 0.1
*/
public class BatchMergeIntegrationTest extends WalkerTest { public class MappingQualityUnavailableReadFilter extends ReadFilter {
@Test public boolean filterOut(SAMRecord rec) {
public void testBatchMerge1() { return (rec.getMappingQuality() == QualityUtils.MAPPING_QUALITY_UNAVAILABLE);
String bam = validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.bam";
String alleles = validationDataLocation + "batch.merge.alleles.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T UnifiedGenotyper -NO_HEADER -BTI alleles -stand_call_conf 0.0 -glm BOTH -G none -nsl -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -o %s -R " + b37KGReference
+ " -B:alleles,VCF " + alleles
+ " -I " + bam,
1,
Arrays.asList("f4ed8f4ef2cba96823c06e90e9d0de35"));
executeTest("testBatchMerge UG genotype given alleles:" + new File(bam).getName() + " with " + new File(alleles).getName(), spec);
} }
} }

5
public/java/src/org/broadinstitute/sting/gatk/filters/ZeroMappingQualityReadFilter.java → public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityZeroReadFilter.java
View File

@ -24,17 +24,16 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
/** /**
* Filter out zero mapping quality reads. * Filter out mapping quality zero reads.
* *
* @author hanna * @author hanna
* @version 0.1 * @version 0.1
*/ */
public class ZeroMappingQualityReadFilter extends ReadFilter { public class MappingQualityZeroReadFilter extends ReadFilter {
public boolean filterOut(SAMRecord rec) { public boolean filterOut(SAMRecord rec) {
return (rec.getMappingQuality() == 0); return (rec.getMappingQuality() == 0);
} }

1
public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java
View File

@ -1,6 +1,5 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;

1
public/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java
View File

@ -25,7 +25,6 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;

1
public/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java
View File

@ -24,7 +24,6 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
/** /**

1
public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java
View File

@ -1,6 +1,5 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
/* /*

1
public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentReadFilter.java
View File

@ -24,7 +24,6 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
/** /**

2
public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java
View File

@ -25,9 +25,7 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.sam.ReadUtils;
/** /**

4
public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java
View File

@ -25,11 +25,9 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.sam.ReadUtils;
/** /**
* Filter out PL matching reads. * Filter out PL matching reads.

10
public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java
View File

@ -1,14 +1,12 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import java.util.Set;
import java.util.HashSet;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import java.util.HashSet;
import java.util.Set;
/** /**
* Created by IntelliJ IDEA. * Created by IntelliJ IDEA.
* User: asivache * User: asivache

1
public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java
View File

@ -1,7 +1,6 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter; import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
/** /**

13
public/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java
View File

@ -25,17 +25,16 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import java.util.*;
import java.util.Map.Entry;
import java.io.File;
import java.io.FileNotFoundException;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.text.XReadLines; import org.broadinstitute.sting.utils.text.XReadLines;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.*;
import java.util.Map.Entry;
/** /**
* Removes records matching the read group tag and exact match string. * Removes records matching the read group tag and exact match string.
* For example, this filter value: * For example, this filter value:

1
public/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java
View File

@ -25,7 +25,6 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;

3
public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java
View File

@ -25,9 +25,8 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import java.util.Set; import java.util.Set;

3
public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java
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@ -25,9 +25,8 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMReadGroupRecord;
import net.sf.picard.filter.SamRecordFilter; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
/** /**

1
public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java
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@ -24,7 +24,6 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
/** /**

4
public/java/src/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java
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@ -25,9 +25,9 @@
package org.broadinstitute.sting.gatk.io; package org.broadinstitute.sting.gatk.io;
import org.broadinstitute.sting.gatk.io.stubs.Stub;
import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
import org.broadinstitute.sting.gatk.io.storage.Storage; import org.broadinstitute.sting.gatk.io.storage.Storage;
import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
import org.broadinstitute.sting.gatk.io.stubs.Stub;
/** /**
* Maps creation of storage directly to output streams in parent. * Maps creation of storage directly to output streams in parent.

16
public/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
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@ -26,20 +26,20 @@
package org.broadinstitute.sting.gatk.io; package org.broadinstitute.sting.gatk.io;
import net.sf.samtools.SAMFileReader; import net.sf.samtools.SAMFileReader;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.commandline.ArgumentSource; import org.broadinstitute.sting.commandline.ArgumentSource;
import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder; import org.broadinstitute.sting.gatk.io.storage.Storage;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub; import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
import org.broadinstitute.sting.gatk.io.stubs.Stub; import org.broadinstitute.sting.gatk.io.stubs.Stub;
import org.broadinstitute.sting.gatk.io.storage.StorageFactory; import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.io.storage.Storage; import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
import java.io.*; import java.io.OutputStream;
import java.lang.reflect.Field; import java.lang.reflect.Field;
import java.util.Map;
import java.util.HashMap; import java.util.HashMap;
import java.util.Map;
/** /**
* Manages the output and err streams that are created specifically for walker * Manages the output and err streams that are created specifically for walker

2
public/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java
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@ -1,7 +1,7 @@
package org.broadinstitute.sting.gatk.io; package org.broadinstitute.sting.gatk.io;
import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileWriter;
/** /**
* A writer that will allow unsorted BAM files to be written * A writer that will allow unsorted BAM files to be written

9
public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java
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@ -25,15 +25,16 @@
package org.broadinstitute.sting.gatk.io; package org.broadinstitute.sting.gatk.io;
import org.broadinstitute.sting.gatk.io.stubs.Stub;
import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
import org.broadinstitute.sting.gatk.io.storage.Storage;
import org.broadinstitute.sting.gatk.executive.OutputMergeTask; import org.broadinstitute.sting.gatk.executive.OutputMergeTask;
import org.broadinstitute.sting.gatk.io.storage.Storage;
import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
import org.broadinstitute.sting.gatk.io.stubs.Stub;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import java.util.*;
import java.io.File; import java.io.File;
import java.io.IOException; import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
/** /**
* An output tracker that can either track its output per-thread or directly, * An output tracker that can either track its output per-thread or directly,

4
public/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
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@ -25,14 +25,14 @@
package org.broadinstitute.sting.gatk.io.storage; package org.broadinstitute.sting.gatk.io.storage;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub; import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.*; import java.io.*;
import java.nio.channels.Channels;
import java.nio.channels.FileChannel; import java.nio.channels.FileChannel;
import java.nio.channels.WritableByteChannel; import java.nio.channels.WritableByteChannel;
import java.nio.channels.Channels;
public class OutputStreamStorage extends OutputStream implements Storage<OutputStream> { public class OutputStreamStorage extends OutputStream implements Storage<OutputStream> {
/** /**

9
public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
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@ -27,17 +27,16 @@ package org.broadinstitute.sting.gatk.io.storage;
import net.sf.samtools.*; import net.sf.samtools.*;
import net.sf.samtools.util.CloseableIterator; import net.sf.samtools.util.CloseableIterator;
import java.io.*;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import net.sf.samtools.util.RuntimeIOException; import net.sf.samtools.util.RuntimeIOException;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub; import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.SimplifyingSAMFileWriter; import org.broadinstitute.sting.utils.sam.SimplifyingSAMFileWriter;
import java.io.File;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
/** /**
* Provides temporary storage for SAMFileWriters. * Provides temporary storage for SAMFileWriters.
* *

2
public/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java
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@ -25,9 +25,9 @@
package org.broadinstitute.sting.gatk.io.storage; package org.broadinstitute.sting.gatk.io.storage;
import org.broadinstitute.sting.gatk.io.stubs.Stub;
import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub; import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub; import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
import org.broadinstitute.sting.gatk.io.stubs.Stub;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub; import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;

19
public/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
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@ -1,16 +1,21 @@
package org.broadinstitute.sting.gatk.io.storage; package org.broadinstitute.sting.gatk.io.storage;
import net.sf.samtools.util.BlockCompressedOutputStream;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broad.tribble.source.BasicFeatureSource; import org.broad.tribble.source.BasicFeatureSource;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub; import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter;
import java.io.*; import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import net.sf.samtools.util.BlockCompressedOutputStream; import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.File;
import java.io.IOException;
import java.io.OutputStream;
import java.io.PrintStream;
/** /**
* Provides temporary and permanent storage for genotypes in VCF format. * Provides temporary and permanent storage for genotypes in VCF format.

2
public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java
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@ -30,8 +30,8 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.OutputStream;
import java.io.File; import java.io.File;
import java.io.OutputStream;
import java.lang.reflect.Constructor; import java.lang.reflect.Constructor;
/** /**

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