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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Eric Banks 2011-10-26 15:44:25 -04:00
parent b6ce6ed3f8 751d66174a
commit b39fcb1bea
123 changed files with 4445 additions and 1901 deletions
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20
.gitignore vendored 100644
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@ -0,0 +1,20 @@
/*.bam
/*.bai
/*.bed
*.idx
*~
/*.vcf
/*.txt
/*.csh
/.*
/*.pdf
/*.eval
*.ipr
*.iws
*.iml
.DS_Store
queueScatterGather
/foo*
/bar*
integrationtests/
public/testdata/onTheFlyOutputTest.vcf

138
build.xml
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@ -28,6 +28,8 @@
<property name="build.dir" value="build" />
<property name="dist.dir" value="dist" />
<property name="contract.dump.dir" value="dump" />
<property name="pipelinetest.dir" value="pipelinetests" />
<property name="lib.dir" value="lib" />
<property name="external.dir" value="external" />
<property name="public.dir" value="public" />
@ -35,18 +37,25 @@
<property name="java.public.source.dir" value="${public.dir}/java/src" />
<property name="java.private.source.dir" value="${private.dir}/java/src" />
<property name="java.classes" value="${build.dir}/java/classes" />
<property name="R.public.scripts.dir" value="${public.dir}/R/scripts" />
<property name="R.public.src.dir" value="${public.dir}/R/src" />
<!-- Legacy: Installing libraries back into the source directory
instead of the build or dist directory... intentionally avoids ant clean?? -->
<property name="R.library.dir" value="${public.dir}/R" />
<property name="R.tar.dir" value="${build.dir}/R/src" />
<property name="R.package.path" value="org/broadinstitute/sting/utils/R" />
<property name="resource.file" value="StingText.properties" />
<property name="resource.path" value="${java.classes}/StingText.properties" />
<property name="scala.public.source.dir" value="${public.dir}/scala/src" />
<property name="scala.private.source.dir" value="${private.dir}/scala/src" />
<property name="scala.private.source.dir" value="${private.dir}/scala/src" />
<property name="scala.classes" value="${build.dir}/scala/classes" />
<property name="queue-extensions.source.dir" value="${build.dir}/queue-extensions/src" />
<property name="javadoc.dir" value="javadoc" />
<property name="scaladoc.dir" value="scaladoc" />
<!-- Contracts for Java -->
<!-- By default, enabled only for test targets -->
<!-- To disable for test targets, run with -Duse.contracts=false -->
@ -60,7 +69,7 @@
<!-- do we want to halt on failure of a unit test? default to yes (Bamboo uses 'no') -->
<property name="halt" value="yes" />
<!-- should our unit test output go to a file or the screen?
false means it goes to the screen (default) true to file -->
<property name="usefile" value="false" />
@ -82,7 +91,7 @@
<patternset refid="java.source.pattern" />
</fileset>
<!-- terrible hack to get gatkdocs to see all files -->
<!-- terrible hack to get gatkdocs to see all files -->
<patternset id="all.java.source.pattern">
<include name="${java.public.source.dir}/**/*.java" />
<include name="${java.private.source.dir}/**/*.java" />
@ -113,7 +122,7 @@
<exclude name="testng*.jar" />
<exclude name="bcel*.jar" />
</patternset>
<path id="external.dependencies">
<fileset dir="${lib.dir}">
<patternset refid="dependency.mask" />
@ -154,7 +163,7 @@
<property name="ivy.jar.file" value="ivy-${ivy.install.version}.jar"/>
<property name="ivy.settings.dir" value="settings"/>
<property file="${ivy.settings.dir}/ivysettings.properties"/>
<mkdir dir="${lib.dir}"/>
<mkdir dir="${ivy.jar.dir}"/>
@ -211,11 +220,11 @@
<equals arg1="${git.describe.exit.value}" arg2="0" />
</condition>
</target>
<target name="tagged.build.version" depends="git.describe" if="git.describe.succeeded">
<property name="build.version" value="${git.describe.output}" />
</target>
<target name="git.rev-parse" depends="git.describe" unless="git.describe.succeeded">
<exec executable="git" outputproperty="git.rev-parse.output" resultproperty="git.rev-parse.exit.value" failonerror="false">
<arg line="rev-parse HEAD" />
@ -224,11 +233,11 @@
<equals arg1="${git.rev-parse.exit.value}" arg2="0" />
</condition>
</target>
<target name="untagged.build.version" depends="git.rev-parse" if="git.rev-parse.succeeded">
<property name="build.version" value="${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" />
@ -266,7 +275,7 @@
<echo message="Scala build : ${scala.target}"/>
<echo message="source revision : ${build.version}"/>
<echo message="build time : ${build.timestamp}" />
<condition property="include.private">
<equals arg1="${gatk.target}" arg2="private" casesensitive="false" />
</condition>
@ -312,13 +321,13 @@
<target name="gatk.compile.public.source" depends="init,resolve">
<javac fork="true" srcdir="${java.public.source.dir}" memoryMaximumSize="512m" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies" tempdir="${java.io.tmpdir}">
<compilerarg value="-proc:none"/>
</javac>
</javac>
</target>
<target name="gatk.compile.private.source" depends="gatk.compile.public.source" if="include.private">
<javac fork="true" srcdir="${java.private.source.dir}" memoryMaximumSize="512m" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies" tempdir="${java.io.tmpdir}">
<compilerarg value="-proc:none"/>
</javac>
</javac>
</target>
<target name="gatk.compile.external.source" depends="gatk.compile.public.source,gatk.compile.private.source">
@ -327,11 +336,11 @@
<property name="dist.dir" value="${external.dist.dir}" />
<property name="gatk.classpath" value="${external.gatk.classpath}" />
<fileset dir="${external.dir}" includes="*/build.xml" erroronmissingdir="false" />
</subant>
</subant>
</target>
<target name="gatk.compile.source"
depends="gatk.compile.public.source,gatk.compile.private.source,gatk.compile.external.source"
<target name="gatk.compile.source"
depends="gatk.compile.public.source,gatk.compile.private.source,gatk.compile.external.source"
description="compile the GATK source" />
<target name="gatk.contracts.public" depends="gatk.compile.source" if="include.contracts">
@ -341,9 +350,9 @@
<pathelement path="${java.classes}" />
</classpath>
<compilerarg value="-Acom.google.java.contract.debug"/>
<compilerarg value="-Acom.google.java.contract.dump=dump/"/>
<compilerarg value="-Acom.google.java.contract.dump=${contract.dump.dir}"/>
<compilerarg value="-proc:only"/>
</javac>
</javac>
</target>
<target name="check.contracts.private" depends="gatk.contracts.public">
@ -362,14 +371,14 @@
<pathelement path="${java.classes}" />
</classpath>
<compilerarg value="-Acom.google.java.contract.debug"/>
<compilerarg value="-Acom.google.java.contract.dump=dump/"/>
<compilerarg value="-Acom.google.java.contract.dump=${contract.dump.dir}"/>
<compilerarg value="-proc:only"/>
</javac>
</javac>
</target>
<target name="gatk.contracts" depends="gatk.contracts.public,gatk.contracts.private"
<target name="gatk.contracts" depends="gatk.contracts.public,gatk.contracts.private"
description="create GATK contracts" if="include.contracts" />
<target name="gatk.compile" depends="init,resolve,gatk.compile.source,gatk.contracts" />
<target name="init.queue-extensions.generate" depends="gatk.compile">
@ -413,9 +422,9 @@
<src path="${scala.public.source.dir}" />
<src path="${queue-extensions.source.dir}" />
<include name="**/*.scala"/>
</scalac>
</scalac>
</target>
<target name="check.scala.private" depends="scala.compile.public">
<condition property="include.scala.private">
<and>
@ -424,12 +433,12 @@
</and>
</condition>
</target>
<target name="scala.compile.private" depends="check.scala.private" if="include.scala.private">
<scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.classes}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
<src path="${scala.private.source.dir}" />
<include name="**/*.scala"/>
</scalac>
</scalac>
</target>
<target name="scala.compile" depends="scala.compile.public,scala.compile.private" if="scala.include" description="compile Scala" />
@ -532,6 +541,11 @@
<target name="sting.compile" depends="gatk.compile, scala.compile" />
<target name="R.public.tar">
<mkdir dir="${R.tar.dir}/${R.package.path}" />
<tar compression="gzip" basedir="${R.public.src.dir}/${R.package.path}" includes="gsalib/**" destfile="${R.tar.dir}/${R.package.path}/gsalib.tar.gz" />
</target>
<target name="init.jar" depends="sting.compile,extracthelp">
<mkdir dir="${dist.dir}"/>
<copy todir="${dist.dir}">
@ -539,7 +553,7 @@
</copy>
</target>
<target name="sting-utils.jar" depends="gatk.compile, init.jar">
<target name="sting-utils.jar" depends="gatk.compile, init.jar, R.public.tar">
<jar jarfile="${dist.dir}/StingUtils.jar">
<fileset dir="${java.classes}">
<include name="**/utils/**/*.class"/>
@ -551,6 +565,12 @@
<fileset dir="${java.classes}" includes="**/sting/jna/**/*.class"/>
<fileset dir="${java.classes}" includes="net/sf/picard/**/*.class"/>
<fileset dir="${java.classes}" includes="net/sf/samtools/**/*.class"/>
<fileset dir="${R.tar.dir}">
<include name="**/${R.package.path}/**/*.tar.gz"/>
</fileset>
<fileset dir="${R.public.scripts.dir}">
<include name="**/utils/**/*.R"/>
</fileset>
<manifest>
<attribute name="Premain-Class" value="org.broadinstitute.sting.utils.instrumentation.Sizeof" />
</manifest>
@ -579,6 +599,10 @@
<include name="**/gatk/**/*.class" />
<include name="**/alignment/**/*.class"/>
</fileset>
<fileset dir="${R.public.scripts.dir}">
<include name="**/gatk/**/*.R"/>
<include name="**/alignment/**/*.R"/>
</fileset>
<manifest>
<attribute name="Main-Class" value="org.broadinstitute.sting.gatk.CommandLineGATK" />
</manifest>
@ -593,6 +617,10 @@
<include name="**/analyzecovariates/**/*.class" />
<include name="**/gatk/walkers/recalibration/*.class" />
</fileset>
<fileset dir="${R.public.scripts.dir}">
<include name="**/analyzecovariates/**/*.R"/>
<include name="**/gatk/walkers/recalibration/**/*.R"/>
</fileset>
<manifest>
<attribute name="Main-Class" value="org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates" />
</manifest>
@ -605,28 +633,7 @@
<fileset dir="${external.dir}" includes="*/build.xml" erroronmissingdir="false" />
</subant>
</target>
<!--
<target name="gatk.oneoffs.jar" depends="gatk.compile, init.jar"
description="generate the GATK oneoffs distribution" if="include.oneoffs">
<jar jarfile="${dist.dir}/CompareBAMAlignments.jar" whenmanifestonly="skip">
<fileset dir="${java.classes}">
<include name="**/tools/**/*.class" />
</fileset>
<manifest>
<attribute name="Main-Class" value="org.broadinstitute.sting.oneoffprojects.tools.CompareBAMAlignments" />
</manifest>
</jar>
<jar jarfile="${dist.dir}/SliceBams.jar" whenmanifestonly="skip">
<fileset dir="${java.classes}">
<include name="**/tools/**/*.class" />
</fileset>
<manifest>
<attribute name="Main-Class" value="org.broadinstitute.sting.playground.tools.SliceBams" />
</manifest>
</jar>
</target>
-->
<target name="scala.jar" depends="scala.compile, init.jar" if="scala.include">
<jar jarfile="${dist.dir}/GATKScala.jar">
<fileset dir="${scala.classes}">
@ -643,6 +650,9 @@
<fileset dir="${java.classes}">
<include name="org/broadinstitute/sting/queue/**/*.class" />
</fileset>
<fileset dir="${R.public.scripts.dir}">
<include name="org/broadinstitute/sting/queue/**/*.R"/>
</fileset>
<manifest>
<attribute name="Main-Class" value="org.broadinstitute.sting.queue.QCommandLine" />
</manifest>
@ -682,20 +692,7 @@
</jar>
</target>
<!--
<target name="gatk.oneoffs.manifests" depends="gatk.oneoffs.jar, init.manifests" if="include.oneoffs">
<jar jarfile="${dist.dir}/CompareBAMAlignments.jar" update="true" whenmanifestonly="skip">
<manifest>
<attribute name="Class-Path" value="${jar.classpath}" />
</manifest>
</jar>
<jar jarfile="${dist.dir}/SliceBams.jar" update="true" whenmanifestonly="skip">
<manifest>
<attribute name="Class-Path" value="${jar.classpath}" />
</manifest>
</jar>
</target>
-->
<target name="queue.manifests" depends="queue.jar, init.manifests" if="scala.include">
<jar jarfile="${dist.dir}/Queue.jar" update="true" >
<manifest>
@ -780,10 +777,6 @@
<pathelement location="${testng.jar}"/>
</classpath>
<compilerarg value="-proc:none"/>
<!--
<compilerarg value="-Acom.google.java.contract.debug"/>
<compilerarg value="-Acom.google.java.contract.dump=dump/"/>
-->
</javac>
</target>
@ -800,10 +793,6 @@
<pathelement location="${testng.jar}"/>
</classpath>
<compilerarg value="-proc:none"/>
<!--
<compilerarg value="-Acom.google.java.contract.debug"/>
<compilerarg value="-Acom.google.java.contract.dump=dump/"/>
-->
</javac>
</target>
@ -851,6 +840,8 @@
<pathelement location="${java.private.test.classes}" />
<pathelement location="${scala.public.test.classes}" />
<pathelement location="${scala.private.test.classes}" />
<pathelement location="${R.tar.dir}" />
<pathelement location="${R.public.scripts.dir}" />
</path>
<path id="testng.gatk.releasetest.classpath">
@ -1187,19 +1178,18 @@
</target>
<target name="clean" description="clean up" depends="clean.javadoc,clean.scaladoc,clean.gatkdocs">
<delete dir="out"/>
<delete dir="${build.dir}"/>
<delete dir="${lib.dir}"/>
<delete dir="dump"/>
<delete dir="${contract.dump.dir}"/>
<delete dir="${staging.dir}"/>
<delete dir="${dist.dir}"/>
<delete dir="pipelinetests"/>
<delete dir="${pipelinetest.dir}"/>
</target>
<!-- Build gsalib R module -->
<target name="gsalib">
<exec executable="R" failonerror="true">
<arg line="R CMD INSTALL -l public/R/ public/R/src/gsalib/" />
<arg line="R CMD INSTALL -l ${R.library.dir} ${R.public.src.dir}/${R.package.path}/gsalib" />
</exec>
</target>
</project>

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public/R/queueJobReport.R → public/R/scripts/org/broadinstitute/sting/queue/util/queueJobReport.R
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public/R/src/gsalib/DESCRIPTION → public/R/src/org/broadinstitute/sting/utils/R/gsalib/DESCRIPTION
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public/R/src/gsalib/R/gsa.error.R → public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.error.R
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public/R/src/gsalib/R/gsa.getargs.R → public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.getargs.R
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public/R/src/gsalib/R/gsa.read.gatkreport.R → public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.gatkreport.R
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public/R/src/gsalib/R/gsa.read.squidmetrics.R → public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.squidmetrics.R
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public/R/src/gsalib/R/gsa.read.vcf.R → public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.vcf.R
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public/R/src/gsalib/R/gsa.warn.R → public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.warn.R
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public/R/src/gsalib/Read-and-delete-me → public/R/src/org/broadinstitute/sting/utils/R/gsalib/Read-and-delete-me
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public/R/src/gsalib/man/gsa.error.Rd → public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.error.Rd
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public/R/src/gsalib/man/gsa.getargs.Rd → public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.getargs.Rd
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public/R/src/gsalib/man/gsa.message.Rd → public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.message.Rd
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public/R/src/gsalib/man/gsa.read.eval.Rd → public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.eval.Rd
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public/R/src/gsalib/man/gsa.read.gatkreport.Rd → public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.gatkreport.Rd
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public/R/src/gsalib/man/gsa.read.squidmetrics.Rd → public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.squidmetrics.Rd
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public/R/src/gsalib/man/gsa.read.vcf.Rd → public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.vcf.Rd
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public/R/src/gsalib/man/gsa.warn.Rd → public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.warn.Rd
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public/R/src/gsalib/man/gsalib-package.Rd → public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsalib-package.Rd
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83
public/java/src/org/broadinstitute/sting/commandline/ArgumentMatch.java
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@ -46,7 +46,7 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
/**
* Maps indices of command line arguments to values paired with that argument.
*/
public final SortedMap<Integer,List<String>> indices = new TreeMap<Integer,List<String>>();
public final SortedMap<ArgumentMatchSite,List<String>> sites = new TreeMap<ArgumentMatchSite,List<String>>();
/**
* An ordered, freeform collection of tags.
@ -72,32 +72,32 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
}
/**
* A simple way of indicating that an argument with the given label and definition exists at this index.
* A simple way of indicating that an argument with the given label and definition exists at this site.
* @param label Label of the argument match. Must not be null.
* @param definition The associated definition, if one exists. May be null.
* @param index Position of the argument. Must not be null.
* @param site Position of the argument. Must not be null.
* @param tags ordered freeform text tags associated with this argument.
*/
public ArgumentMatch(final String label, final ArgumentDefinition definition, final int index, final Tags tags) {
this( label, definition, index, null, tags );
public ArgumentMatch(final String label, final ArgumentDefinition definition, final ArgumentMatchSite site, final Tags tags) {
this( label, definition, site, null, tags );
}
/**
* A simple way of indicating that an argument with the given label and definition exists at this index.
* A simple way of indicating that an argument with the given label and definition exists at this site.
* @param label Label of the argument match. Must not be null.
* @param definition The associated definition, if one exists. May be null.
* @param index Position of the argument. Must not be null.
* @param site Position of the argument. Must not be null.
* @param value Value for the argument at this position.
* @param tags ordered freeform text tags associated with this argument.
*/
private ArgumentMatch(final String label, final ArgumentDefinition definition, final int index, final String value, final Tags tags) {
private ArgumentMatch(final String label, final ArgumentDefinition definition, final ArgumentMatchSite site, final String value, final Tags tags) {
this.label = label;
this.definition = definition;
ArrayList<String> values = new ArrayList<String>();
if( value != null )
values.add(value);
indices.put(index,values );
sites.put(site,values );
this.tags = tags;
}
@ -117,7 +117,7 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
ArgumentMatch otherArgumentMatch = (ArgumentMatch)other;
return this.definition.equals(otherArgumentMatch.definition) &&
this.label.equals(otherArgumentMatch.label) &&
this.indices.equals(otherArgumentMatch.indices) &&
this.sites.equals(otherArgumentMatch.sites) &&
this.tags.equals(otherArgumentMatch.tags);
}
@ -129,16 +129,17 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
* @param key Key which specifies the transform.
* @return A variant of this ArgumentMatch with all keys transformed.
*/
@SuppressWarnings("unchecked")
ArgumentMatch transform(Multiplexer multiplexer, Object key) {
SortedMap<Integer,List<String>> newIndices = new TreeMap<Integer,List<String>>();
for(Map.Entry<Integer,List<String>> index: indices.entrySet()) {
SortedMap<ArgumentMatchSite,List<String>> newIndices = new TreeMap<ArgumentMatchSite,List<String>>();
for(Map.Entry<ArgumentMatchSite,List<String>> site: sites.entrySet()) {
List<String> newEntries = new ArrayList<String>();
for(String entry: index.getValue())
for(String entry: site.getValue())
newEntries.add(multiplexer.transformArgument(key,entry));
newIndices.put(index.getKey(),newEntries);
newIndices.put(site.getKey(),newEntries);
}
ArgumentMatch newArgumentMatch = new ArgumentMatch(label,definition);
newArgumentMatch.indices.putAll(newIndices);
newArgumentMatch.sites.putAll(newIndices);
return newArgumentMatch;
}
@ -157,9 +158,9 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
public Iterator<ArgumentMatch> iterator() {
return new Iterator<ArgumentMatch>() {
/**
* Iterate over each the available index.
* Iterate over each the available site.
*/
private Iterator<Integer> indexIterator = null;
private Iterator<ArgumentMatchSite> siteIterator = null;
/**
* Iterate over each available token.
@ -167,9 +168,9 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
private Iterator<String> tokenIterator = null;
/**
* The next index to return. Null if none remain.
* The next site to return. Null if none remain.
*/
Integer nextIndex = null;
ArgumentMatchSite nextSite = null;
/**
* The next token to return. Null if none remain.
@ -177,7 +178,7 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
String nextToken = null;
{
indexIterator = indices.keySet().iterator();
siteIterator = sites.keySet().iterator();
prepareNext();
}
@ -186,7 +187,7 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
* @return True if there's another token waiting in the wings. False otherwise.
*/
public boolean hasNext() {
return nextToken != null;
return nextToken != null;
}
/**
@ -194,32 +195,32 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
* @return The next ArgumentMatch in the series. Should never be null.
*/
public ArgumentMatch next() {
if( nextIndex == null || nextToken == null )
if( nextSite == null || nextToken == null )
throw new IllegalStateException( "No more ArgumentMatches are available" );
ArgumentMatch match = new ArgumentMatch( label, definition, nextIndex, nextToken, tags );
ArgumentMatch match = new ArgumentMatch( label, definition, nextSite, nextToken, tags );
prepareNext();
return match;
}
/**
* Initialize the next ArgumentMatch to return. If no ArgumentMatches are available,
* initialize nextIndex / nextToken to null.
* initialize nextSite / nextToken to null.
*/
private void prepareNext() {
if( tokenIterator != null && tokenIterator.hasNext() ) {
nextToken = tokenIterator.next();
}
else {
nextIndex = null;
nextSite = null;
nextToken = null;
// Do a nested loop. While more data is present in the inner loop, grab that data.
// Otherwise, troll the outer iterator looking for more data.
while( indexIterator.hasNext() ) {
nextIndex = indexIterator.next();
if( indices.get(nextIndex) != null ) {
tokenIterator = indices.get(nextIndex).iterator();
while( siteIterator.hasNext() ) {
nextSite = siteIterator.next();
if( sites.get(nextSite) != null ) {
tokenIterator = sites.get(nextSite).iterator();
if( tokenIterator.hasNext() ) {
nextToken = tokenIterator.next();
break;
@ -245,29 +246,29 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
* @param other The other match to merge into.
*/
public void mergeInto( ArgumentMatch other ) {
indices.putAll(other.indices);
sites.putAll(other.sites);
}
/**
* Associate a value with this merge maapping.
* @param index index of the command-line argument to which this value is mated.
* @param site site of the command-line argument to which this value is mated.
* @param value Text representation of value to add.
*/
public void addValue( int index, String value ) {
if( !indices.containsKey(index) || indices.get(index) == null )
indices.put(index, new ArrayList<String>() );
indices.get(index).add(value);
public void addValue( ArgumentMatchSite site, String value ) {
if( !sites.containsKey(site) || sites.get(site) == null )
sites.put(site, new ArrayList<String>() );
sites.get(site).add(value);
}
/**
* Does this argument already have a value at the given site?
* Arguments are only allowed to be single-valued per site, and
* flags aren't allowed a value at all.
* @param index Index at which to check for values.
* @param site Site at which to check for values.
* @return True if the argument has a value at the given site. False otherwise.
*/
public boolean hasValueAtSite( int index ) {
return (indices.get(index) != null && indices.get(index).size() >= 1) || isArgumentFlag();
public boolean hasValueAtSite( ArgumentMatchSite site ) {
return (sites.get(site) != null && sites.get(site).size() >= 1) || isArgumentFlag();
}
/**
@ -276,9 +277,9 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
*/
public List<String> values() {
List<String> values = new ArrayList<String>();
for( int index: indices.keySet() ) {
if( indices.get(index) != null )
values.addAll(indices.get(index));
for( ArgumentMatchSite site: sites.keySet() ) {
if( sites.get(site) != null )
values.addAll(sites.get(site));
}
return values;
}

76
public/java/src/org/broadinstitute/sting/commandline/ArgumentMatchSite.java 100644
View File

@ -0,0 +1,76 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.commandline;
/**
* Which source and the index within the source where an argument match was found.
*/
public class ArgumentMatchSite implements Comparable<ArgumentMatchSite> {
private final ArgumentMatchSource source;
private final int index;
public ArgumentMatchSite(ArgumentMatchSource source, int index) {
this.source = source;
this.index = index;
}
public ArgumentMatchSource getSource() {
return source;
}
public int getIndex() {
return index;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
ArgumentMatchSite that = (ArgumentMatchSite) o;
return (index == that.index) && (source == null ? that.source == null : source.equals(that.source));
}
@Override
public int hashCode() {
int result = source != null ? source.hashCode() : 0;
// Generated by intellij. No other special reason to this implementation. -ks
result = 31 * result + index;
return result;
}
@Override
public int compareTo(ArgumentMatchSite that) {
int comp = this.source.compareTo(that.source);
if (comp != 0)
return comp;
// Both files are the same.
if (this.index == that.index)
return 0;
return this.index < that.index ? -1 : 1;
}
}

98
public/java/src/org/broadinstitute/sting/commandline/ArgumentMatchSource.java 100644
View File

@ -0,0 +1,98 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.commandline;
import java.io.File;
/**
* Where an argument match originated, via the commandline or a file.
*/
public class ArgumentMatchSource implements Comparable<ArgumentMatchSource> {
public static final ArgumentMatchSource COMMAND_LINE = new ArgumentMatchSource(ArgumentMatchSourceType.CommandLine, null);
private final ArgumentMatchSourceType type;
private final File file;
/**
* Creates an argument match source from the specified file.
* @param file File specifying the arguments. Must not be null.
*/
public ArgumentMatchSource(File file) {
this(ArgumentMatchSourceType.File, file);
}
private ArgumentMatchSource(ArgumentMatchSourceType type, File file) {
if (type == ArgumentMatchSourceType.File && file == null)
throw new IllegalArgumentException("An argument match source of type File cannot have a null file.");
this.type = type;
this.file = file;
}
public ArgumentMatchSourceType getType() {
return type;
}
public File getFile() {
return file;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
ArgumentMatchSource that = (ArgumentMatchSource) o;
return (type == that.type) && (file == null ? that.file == null : file.equals(that.file));
}
@Override
public int hashCode() {
int result = type != null ? type.hashCode() : 0;
result = 31 * result + (file != null ? file.hashCode() : 0);
return result;
}
/**
* Compares two sources, putting the command line first, then files.
*/
@Override
public int compareTo(ArgumentMatchSource that) {
int comp = this.type.compareTo(that.type);
if (comp != 0)
return comp;
File f1 = this.file;
File f2 = that.file;
if ((f1 == null) ^ (f2 == null)) {
// If one of the files is null and the other is not
// put the null file first
return f1 == null ? -1 : 1;
}
return f1 == null ? 0 : f1.compareTo(f2);
}
}

32
public/java/src/org/broadinstitute/sting/commandline/ArgumentMatchSourceType.java 100644
View File

@ -0,0 +1,32 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.commandline;
/**
* Type of where an argument match originated, via the commandline or a file.
*/
public enum ArgumentMatchSourceType {
CommandLine, File
}

16
public/java/src/org/broadinstitute/sting/commandline/ArgumentMatches.java
View File

@ -37,7 +37,7 @@ public class ArgumentMatches implements Iterable<ArgumentMatch> {
* Collection matches from argument definition to argument value.
* Package protected access is deliberate.
*/
Map<Integer,ArgumentMatch> argumentMatches = new TreeMap<Integer,ArgumentMatch>();
Map<ArgumentMatchSite,ArgumentMatch> argumentMatches = new TreeMap<ArgumentMatchSite,ArgumentMatch>();
/**
* Provide a place to put command-line argument values that don't seem to belong to
@ -80,7 +80,7 @@ public class ArgumentMatches implements Iterable<ArgumentMatch> {
* @param site Site at which to check.
* @return True if the site has a match. False otherwise.
*/
boolean hasMatch( int site ) {
boolean hasMatch( ArgumentMatchSite site ) {
return argumentMatches.containsKey( site );
}
@ -90,7 +90,7 @@ public class ArgumentMatches implements Iterable<ArgumentMatch> {
* @return The match present at the given site.
* @throws IllegalArgumentException if site does not contain a match.
*/
ArgumentMatch getMatch( int site ) {
ArgumentMatch getMatch( ArgumentMatchSite site ) {
if( !argumentMatches.containsKey(site) )
throw new IllegalArgumentException( "Site does not contain an argument: " + site );
return argumentMatches.get(site);
@ -107,6 +107,7 @@ public class ArgumentMatches implements Iterable<ArgumentMatch> {
/**
* Return all argument matches of this source.
* @param parsingEngine Parsing engine.
* @param argumentSource Argument source to match.
* @return List of all matches.
*/
@ -167,6 +168,7 @@ public class ArgumentMatches implements Iterable<ArgumentMatch> {
* TODO: Generify this.
* @param multiplexer Multiplexer that controls the transformation process.
* @param key Key which specifies the transform.
* @return new argument matches.
*/
ArgumentMatches transform(Multiplexer multiplexer, Object key) {
ArgumentMatches newArgumentMatches = new ArgumentMatches();
@ -187,15 +189,15 @@ public class ArgumentMatches implements Iterable<ArgumentMatch> {
for( ArgumentMatch argumentMatch: getUniqueMatches() ) {
if( argumentMatch.definition == match.definition && argumentMatch.tags.equals(match.tags) ) {
argumentMatch.mergeInto( match );
for( int index: match.indices.keySet() )
argumentMatches.put( index, argumentMatch );
for( ArgumentMatchSite site: match.sites.keySet() )
argumentMatches.put( site, argumentMatch );
definitionExists = true;
}
}
if( !definitionExists ) {
for( int index: match.indices.keySet() )
argumentMatches.put( index, match );
for( ArgumentMatchSite site: match.sites.keySet() )
argumentMatches.put( site, match );
}
}

14
public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
View File

@ -35,10 +35,7 @@ import org.broadinstitute.sting.utils.help.ApplicationDetails;
import org.broadinstitute.sting.utils.help.HelpFormatter;
import java.io.IOException;
import java.util.Collection;
import java.util.Collections;
import java.util.EnumSet;
import java.util.Locale;
import java.util.*;
public abstract class CommandLineProgram {
@ -155,6 +152,7 @@ public abstract class CommandLineProgram {
*
* @param clp the command line program to execute
* @param args the command line arguments passed in
* @param dryRun dry run
* @throws Exception when an exception occurs
*/
@SuppressWarnings("unchecked")
@ -176,6 +174,8 @@ public abstract class CommandLineProgram {
ParsingEngine parser = clp.parser = new ParsingEngine(clp);
parser.addArgumentSource(clp.getClass());
Map<ArgumentMatchSource, List<String>> parsedArgs;
// process the args
if (clp.canAddArgumentsDynamically()) {
// if the command-line program can toss in extra args, fetch them and reparse the arguments.
@ -196,14 +196,14 @@ public abstract class CommandLineProgram {
Class[] argumentSources = clp.getArgumentSources();
for (Class argumentSource : argumentSources)
parser.addArgumentSource(clp.getArgumentSourceName(argumentSource), argumentSource);
parser.parse(args);
parsedArgs = parser.parse(args);
if (isHelpPresent(parser))
printHelpAndExit(clp, parser);
if ( ! dryRun ) parser.validate();
} else {
parser.parse(args);
parsedArgs = parser.parse(args);
if ( ! dryRun ) {
if (isHelpPresent(parser))
@ -230,7 +230,7 @@ public abstract class CommandLineProgram {
}
// regardless of what happens next, generate the header information
HelpFormatter.generateHeaderInformation(clp.getApplicationDetails(), args);
HelpFormatter.generateHeaderInformation(clp.getApplicationDetails(), parsedArgs);
// call the execute
CommandLineProgram.result = clp.execute();

93
public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
View File

@ -26,6 +26,7 @@
package org.broadinstitute.sting.commandline;
import com.google.java.contract.Requires;
import org.apache.commons.io.FileUtils;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
@ -35,6 +36,8 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.ApplicationDetails;
import org.broadinstitute.sting.utils.help.HelpFormatter;
import java.io.File;
import java.io.IOException;
import java.lang.reflect.Field;
import java.util.*;
@ -101,6 +104,8 @@ public class ParsingEngine {
if(clp != null)
argumentTypeDescriptors.addAll(clp.getArgumentTypeDescriptors());
argumentTypeDescriptors.addAll(STANDARD_ARGUMENT_TYPE_DESCRIPTORS);
addArgumentSource(ParsingEngineArgumentFiles.class);
}
/**
@ -149,21 +154,43 @@ public class ParsingEngine {
* command-line arguments to the arguments that are actually
* required.
* @param tokens Tokens passed on the command line.
* @return The parsed arguments by file.
*/
public void parse( String[] tokens ) {
public SortedMap<ArgumentMatchSource, List<String>> parse( String[] tokens ) {
argumentMatches = new ArgumentMatches();
SortedMap<ArgumentMatchSource, List<String>> parsedArgs = new TreeMap<ArgumentMatchSource, List<String>>();
int lastArgumentMatchSite = -1;
List<String> cmdLineTokens = Arrays.asList(tokens);
parse(ArgumentMatchSource.COMMAND_LINE, cmdLineTokens, argumentMatches, parsedArgs);
for( int i = 0; i < tokens.length; i++ ) {
String token = tokens[i];
ParsingEngineArgumentFiles argumentFiles = new ParsingEngineArgumentFiles();
// Load the arguments ONLY into the argument files.
// Validation may optionally run on the rest of the arguments.
loadArgumentsIntoObject(argumentFiles);
for (File file: argumentFiles.files) {
List<String> fileTokens = getArguments(file);
parse(new ArgumentMatchSource(file), fileTokens, argumentMatches, parsedArgs);
}
return parsedArgs;
}
private void parse(ArgumentMatchSource matchSource, List<String> tokens,
ArgumentMatches argumentMatches, SortedMap<ArgumentMatchSource, List<String>> parsedArgs) {
ArgumentMatchSite lastArgumentMatchSite = new ArgumentMatchSite(matchSource, -1);
int i = 0;
for (String token: tokens) {
// If the token is of argument form, parse it into its own argument match.
// Otherwise, pair it with the most recently used argument discovered.
ArgumentMatchSite site = new ArgumentMatchSite(matchSource, i);
if( isArgumentForm(token) ) {
ArgumentMatch argumentMatch = parseArgument( token, i );
ArgumentMatch argumentMatch = parseArgument( token, site );
if( argumentMatch != null ) {
argumentMatches.mergeInto( argumentMatch );
lastArgumentMatchSite = i;
lastArgumentMatchSite = site;
}
}
else {
@ -171,10 +198,31 @@ public class ParsingEngine {
!argumentMatches.getMatch(lastArgumentMatchSite).hasValueAtSite(lastArgumentMatchSite))
argumentMatches.getMatch(lastArgumentMatchSite).addValue( lastArgumentMatchSite, token );
else
argumentMatches.MissingArgument.addValue( i, token );
argumentMatches.MissingArgument.addValue( site, token );
}
i++;
}
parsedArgs.put(matchSource, tokens);
}
private List<String> getArguments(File file) {
try {
if (file.getAbsolutePath().endsWith(".list")) {
return getListArguments(file);
}
} catch (IOException e) {
throw new UserException.CouldNotReadInputFile(file, e);
}
throw new UserException.CouldNotReadInputFile(file, "file extension is not .list");
}
private List<String> getListArguments(File file) throws IOException {
ArrayList<String> argsList = new ArrayList<String>();
for (String line: FileUtils.readLines(file))
argsList.addAll(Arrays.asList(Utils.escapeExpressions(line)));
return argsList;
}
public enum ValidationType { MissingRequiredArgument,
@ -495,7 +543,7 @@ public class ParsingEngine {
* @param position The position of the token in question.
* @return ArgumentMatch associated with this token, or null if no match exists.
*/
private ArgumentMatch parseArgument( String token, int position ) {
private ArgumentMatch parseArgument( String token, ArgumentMatchSite position ) {
if( !isArgumentForm(token) )
throw new IllegalArgumentException( "Token is not recognizable as an argument: " + token );
@ -580,9 +628,21 @@ class UnmatchedArgumentException extends ArgumentException {
private static String formatArguments( ArgumentMatch invalidValues ) {
StringBuilder sb = new StringBuilder();
for( int index: invalidValues.indices.keySet() )
for( String value: invalidValues.indices.get(index) ) {
sb.append( String.format("%nInvalid argument value '%s' at position %d.", value, index) );
for( ArgumentMatchSite site: invalidValues.sites.keySet() )
for( String value: invalidValues.sites.get(site) ) {
switch (site.getSource().getType()) {
case CommandLine:
sb.append( String.format("%nInvalid argument value '%s' at position %d.",
value, site.getIndex()) );
break;
case File:
sb.append( String.format("%nInvalid argument value '%s' in file %s at position %d.",
value, site.getSource().getFile().getAbsolutePath(), site.getIndex()) );
break;
default:
throw new RuntimeException( String.format("Unexpected argument match source type: %s",
site.getSource().getType()));
}
if(value != null && Utils.dupString(' ',value.length()).equals(value))
sb.append(" Please make sure any line continuation backslashes on your command line are not followed by whitespace.");
}
@ -635,4 +695,13 @@ class UnknownEnumeratedValueException extends ArgumentException {
private static String formatArguments(ArgumentDefinition definition, String argumentPassed) {
return String.format("Invalid value %s specified for argument %s; valid options are (%s).", argumentPassed, definition.fullName, Utils.join(",",definition.validOptions));
}
}
}
/**
* Container class to store the list of argument files.
* The files will be parsed after the command line arguments.
*/
class ParsingEngineArgumentFiles {
@Argument(fullName = "arg_file", shortName = "args", doc = "Reads arguments from the specified file", required = false)
public List<File> files = new ArrayList<File>();
}

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

@ -68,7 +68,7 @@ public abstract class ParsingMethod {
* @return An argument match. Definition field will be populated if a match was found or
* empty if no appropriate definition could be found.
*/
public ArgumentMatch match( ArgumentDefinitions definitions, String token, int position ) {
public ArgumentMatch match( ArgumentDefinitions definitions, String token, ArgumentMatchSite position ) {
// If the argument is valid, parse out the argument.
Matcher matcher = pattern.matcher(token);
@ -102,9 +102,7 @@ public abstract class ParsingMethod {
// Try to find a matching argument. If found, label that as the match. If not found, add the argument
// with a null definition.
ArgumentMatch argumentMatch = new ArgumentMatch(argument,argumentDefinition,position,tags);
return argumentMatch;
return new ArgumentMatch(argument,argumentDefinition,position,tags);
}
/**

29
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
View File

@ -221,12 +221,12 @@ public class GenomeAnalysisEngine {
ShardStrategy shardStrategy = getShardStrategy(readsDataSource,microScheduler.getReference(),intervals);
// execute the microscheduler, storing the results
Object result = microScheduler.execute(this.walker, shardStrategy);
return microScheduler.execute(this.walker, shardStrategy);
//monitor.stop();
//logger.info(String.format("Maximum heap size consumed: %d",monitor.getMaxMemoryUsed()));
return result;
//return result;
}
/**
@ -301,6 +301,10 @@ public class GenomeAnalysisEngine {
return method;
}
protected void setDownsamplingMethod(DownsamplingMethod method) {
argCollection.setDownsamplingMethod(method);
}
public BAQ.QualityMode getWalkerBAQQualityMode() { return WalkerManager.getBAQQualityMode(walker); }
public BAQ.ApplicationTime getWalkerBAQApplicationTime() { return WalkerManager.getBAQApplicationTime(walker); }
@ -390,7 +394,9 @@ public class GenomeAnalysisEngine {
/**
* Get the sharding strategy given a driving data source.
*
* @param readsDataSource readsDataSource
* @param drivingDataSource Data on which to shard.
* @param intervals intervals
* @return the sharding strategy
*/
protected ShardStrategy getShardStrategy(SAMDataSource readsDataSource, ReferenceSequenceFile drivingDataSource, GenomeLocSortedSet intervals) {
@ -427,7 +433,7 @@ public class GenomeAnalysisEngine {
return new MonolithicShardStrategy(getGenomeLocParser(), readsDataSource,shardType,region);
}
ShardStrategy shardStrategy = null;
ShardStrategy shardStrategy;
ShardStrategyFactory.SHATTER_STRATEGY shardType;
long SHARD_SIZE = 100000L;
@ -436,6 +442,8 @@ public class GenomeAnalysisEngine {
if (walker instanceof RodWalker) SHARD_SIZE *= 1000;
if (intervals != null && !intervals.isEmpty()) {
if (readsDataSource == null)
throw new IllegalArgumentException("readsDataSource is null");
if(!readsDataSource.isEmpty() && readsDataSource.getSortOrder() != SAMFileHeader.SortOrder.coordinate)
throw new UserException.MissortedBAM(SAMFileHeader.SortOrder.coordinate, "Locus walkers can only traverse coordinate-sorted data. Please resort your input BAM file(s) or set the Sort Order tag in the header appropriately.");
@ -499,7 +507,8 @@ public class GenomeAnalysisEngine {
*/
private void initializeTempDirectory() {
File tempDir = new File(System.getProperty("java.io.tmpdir"));
tempDir.mkdirs();
if (!tempDir.exists() && !tempDir.mkdirs())
throw new UserException.BadTmpDir("Unable to create directory");
}
/**
@ -707,6 +716,7 @@ public class GenomeAnalysisEngine {
* @param reads Reads data source.
* @param reference Reference data source.
* @param rods a collection of the reference ordered data tracks
* @param manager manager
*/
private void validateSourcesAgainstReference(SAMDataSource reads, ReferenceSequenceFile reference, Collection<ReferenceOrderedDataSource> rods, RMDTrackBuilder manager) {
if ((reads.isEmpty() && (rods == null || rods.isEmpty())) || reference == null )
@ -735,15 +745,22 @@ public class GenomeAnalysisEngine {
/**
* Gets a data source for the given set of reads.
*
* @param argCollection arguments
* @param genomeLocParser parser
* @param refReader reader
* @return A data source for the given set of reads.
*/
private SAMDataSource createReadsDataSource(GATKArgumentCollection argCollection, GenomeLocParser genomeLocParser, IndexedFastaSequenceFile refReader) {
DownsamplingMethod method = getDownsamplingMethod();
// Synchronize the method back into the collection so that it shows up when
// interrogating for the downsample method during command line recreation.
setDownsamplingMethod(method);
if ( getWalkerBAQApplicationTime() == BAQ.ApplicationTime.FORBIDDEN && argCollection.BAQMode != BAQ.CalculationMode.OFF)
throw new UserException.BadArgumentValue("baq", "Walker cannot accept BAQ'd base qualities, and yet BAQ mode " + argCollection.BAQMode + " was requested.");
SAMDataSource dataSource = new SAMDataSource(
return new SAMDataSource(
samReaderIDs,
genomeLocParser,
argCollection.useOriginalBaseQualities,
@ -759,14 +776,12 @@ public class GenomeAnalysisEngine {
refReader,
argCollection.defaultBaseQualities,
!argCollection.disableLowMemorySharding);
return dataSource;
}
/**
* Opens a reference sequence file paired with an index. Only public for testing purposes
*
* @param refFile Handle to a reference sequence file. Non-null.
* @return A thread-safe file wrapper.
*/
public void setReferenceDataSource(File refFile) {
this.referenceDataSource = new ReferenceDataSource(refFile);

16
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
View File

@ -138,8 +138,8 @@ public class GATKArgumentCollection {
/**
* Gets the downsampling method explicitly specified by the user. If the user didn't specify
* a default downsampling mechanism, return null.
* @return The explicitly specified downsampling mechanism, or null if none exists.
* a default downsampling mechanism, return the default.
* @return The explicitly specified downsampling mechanism, or the default if none exists.
*/
public DownsamplingMethod getDownsamplingMethod() {
if(downsamplingType == null && downsampleFraction == null && downsampleCoverage == null)
@ -149,6 +149,18 @@ public class GATKArgumentCollection {
return new DownsamplingMethod(downsamplingType,downsampleCoverage,downsampleFraction);
}
/**
* Set the downsampling method stored in the argument collection so that it is read back out when interrogating the command line arguments.
* @param method The downsampling mechanism.
*/
public void setDownsamplingMethod(DownsamplingMethod method) {
if (method == null)
throw new IllegalArgumentException("method is null");
downsamplingType = method.type;
downsampleCoverage = method.toCoverage;
downsampleFraction = method.toFraction;
}
// --------------------------------------------------------------------------------------------------------------
//
// BAQ arguments

8
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
View File

@ -43,6 +43,7 @@ import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.baq.BAQSamIterator;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.GATKSamRecordFactory;
import java.io.File;
import java.lang.reflect.InvocationTargetException;
@ -57,6 +58,8 @@ import java.util.*;
* Converts shards to SAM iterators over the specified region
*/
public class SAMDataSource {
final private static GATKSamRecordFactory factory = new GATKSamRecordFactory();
/** Backing support for reads. */
protected final ReadProperties readProperties;
@ -644,7 +647,9 @@ public class SAMDataSource {
BAQ.QualityMode qmode,
IndexedFastaSequenceFile refReader,
byte defaultBaseQualities) {
wrappedIterator = new ReadFormattingIterator(wrappedIterator, useOriginalBaseQualities, defaultBaseQualities);
if ( useOriginalBaseQualities || defaultBaseQualities >= 0 )
// only wrap if we are replacing the original qualitiies or using a default base quality
wrappedIterator = new ReadFormattingIterator(wrappedIterator, useOriginalBaseQualities, defaultBaseQualities);
// NOTE: this (and other filtering) should be done before on-the-fly sorting
// as there is no reason to sort something that we will end of throwing away
@ -756,6 +761,7 @@ public class SAMDataSource {
public SAMReaders(Collection<SAMReaderID> readerIDs, SAMFileReader.ValidationStringency validationStringency) {
for(SAMReaderID readerID: readerIDs) {
SAMFileReader reader = new SAMFileReader(readerID.samFile);
reader.setSAMRecordFactory(factory);
reader.enableFileSource(true);
reader.enableIndexMemoryMapping(false);
if(!enableLowMemorySharding)

26
public/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java
View File

@ -2,7 +2,6 @@ package org.broadinstitute.sting.gatk.iterators;
import net.sf.samtools.SAMRecord;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
/**
* An iterator which does post-processing of a read, including potentially wrapping
@ -78,7 +77,30 @@ public class ReadFormattingIterator implements StingSAMIterator {
* no next exists.
*/
public SAMRecord next() {
return new GATKSAMRecord(wrappedIterator.next(), useOriginalBaseQualities, defaultBaseQualities);
SAMRecord rec = wrappedIterator.next();
// if we are using default quals, check if we need them, and add if necessary.
// 1. we need if reads are lacking or have incomplete quality scores
// 2. we add if defaultBaseQualities has a positive value
if (defaultBaseQualities >= 0) {
byte reads [] = rec.getReadBases();
byte quals [] = rec.getBaseQualities();
if (quals == null || quals.length < reads.length) {
byte new_quals [] = new byte [reads.length];
for (int i=0; i<reads.length; i++)
new_quals[i] = defaultBaseQualities;
rec.setBaseQualities(new_quals);
}
}
// if we are using original quals, set them now if they are present in the record
if ( useOriginalBaseQualities ) {
byte[] originalQuals = rec.getOriginalBaseQualities();
if ( originalQuals != null )
rec.setBaseQualities(originalQuals);
}
return rec;
}
/**

6
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
View File

@ -68,16 +68,12 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
/**
* Must be overridden by concrete subclasses
* @param tracker rod data
* @param ref reference context
* @param GLs genotype likelihoods
* @param Alleles Alleles corresponding to GLs
* @param log10AlleleFrequencyPriors priors
* @param log10AlleleFrequencyPosteriors array (pre-allocated) to store results
*/
protected abstract void getLog10PNonRef(RefMetaDataTracker tracker,
ReferenceContext ref,
Map<String, Genotype> GLs, List<Allele> Alleles,
protected abstract void getLog10PNonRef(Map<String, Genotype> GLs, List<Allele> Alleles,
double[] log10AlleleFrequencyPriors,
double[] log10AlleleFrequencyPosteriors);

4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
View File

@ -51,9 +51,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
super(UAC, N, logger, verboseWriter);
}
public void getLog10PNonRef(RefMetaDataTracker tracker,
ReferenceContext ref,
Map<String, Genotype> GLs, List<Allele> alleles,
public void getLog10PNonRef(Map<String, Genotype> GLs, List<Allele> alleles,
double[] log10AlleleFrequencyPriors,
double[] log10AlleleFrequencyPosteriors) {
final int numAlleles = alleles.size();

4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java
View File

@ -52,9 +52,7 @@ public class GridSearchAFEstimation extends AlleleFrequencyCalculationModel {
AFMatrix = new AlleleFrequencyMatrix(N);
}
protected void getLog10PNonRef(RefMetaDataTracker tracker,
ReferenceContext ref,
Map<String, Genotype> GLs, List<Allele> alleles,
protected void getLog10PNonRef(Map<String, Genotype> GLs, List<Allele> alleles,
double[] log10AlleleFrequencyPriors,
double[] log10AlleleFrequencyPosteriors) {
initializeAFMatrix(GLs);

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
View File

@ -30,12 +30,10 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.indels.HaplotypeIndelErrorModel;
import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
import org.broadinstitute.sting.utils.pileup.PileupElement;

7
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java
View File

@ -4,6 +4,7 @@ import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import java.util.ArrayList;
import java.util.List;
/**
* Created by IntelliJ IDEA.
@ -15,11 +16,11 @@ import java.util.ArrayList;
public class MultiallelicGenotypeLikelihoods {
private String sample;
private double[] GLs;
private ArrayList<Allele> alleleList;
private List<Allele> alleleList;
private int depth;
public MultiallelicGenotypeLikelihoods(String sample,
ArrayList<Allele> A,
List<Allele> A,
double[] log10Likelihoods, int depth) {
/* Check for consistency between likelihood vector and number of alleles */
int numAlleles = A.size();
@ -40,7 +41,7 @@ public class MultiallelicGenotypeLikelihoods {
return GLs;
}
public ArrayList<Allele> getAlleles() {
public List<Allele> getAlleles() {
return alleleList;
}

80
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -325,7 +325,7 @@ public class UnifiedGenotyperEngine {
// 'zero' out the AFs (so that we don't have to worry if not all samples have reads at this position)
clearAFarray(log10AlleleFrequencyPosteriors.get());
afcm.get().getLog10PNonRef(tracker, refContext, vc.getGenotypes(), vc.getAlleles(), getAlleleFrequencyPriors(model), log10AlleleFrequencyPosteriors.get());
afcm.get().getLog10PNonRef(vc.getGenotypes(), vc.getAlleles(), getAlleleFrequencyPriors(model), log10AlleleFrequencyPosteriors.get());
// find the most likely frequency
int bestAFguess = MathUtils.maxElementIndex(log10AlleleFrequencyPosteriors.get());
@ -383,7 +383,7 @@ public class UnifiedGenotyperEngine {
// the overall lod
VariantContext vcOverall = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, vc.getAlternateAllele(0), false, model);
clearAFarray(log10AlleleFrequencyPosteriors.get());
afcm.get().getLog10PNonRef(tracker, refContext, vcOverall.getGenotypes(), vc.getAlleles(), getAlleleFrequencyPriors(model), log10AlleleFrequencyPosteriors.get());
afcm.get().getLog10PNonRef(vcOverall.getGenotypes(), vc.getAlleles(), getAlleleFrequencyPriors(model), log10AlleleFrequencyPosteriors.get());
//double overallLog10PofNull = log10AlleleFrequencyPosteriors.get()[0];
double overallLog10PofF = MathUtils.log10sumLog10(log10AlleleFrequencyPosteriors.get(), 1);
//if ( DEBUG_SLOD ) System.out.println("overallLog10PofF=" + overallLog10PofF);
@ -391,7 +391,7 @@ public class UnifiedGenotyperEngine {
// the forward lod
VariantContext vcForward = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.FORWARD, vc.getAlternateAllele(0), false, model);
clearAFarray(log10AlleleFrequencyPosteriors.get());
afcm.get().getLog10PNonRef(tracker, refContext, vcForward.getGenotypes(), vc.getAlleles(), getAlleleFrequencyPriors(model), log10AlleleFrequencyPosteriors.get());
afcm.get().getLog10PNonRef(vcForward.getGenotypes(), vc.getAlleles(), getAlleleFrequencyPriors(model), log10AlleleFrequencyPosteriors.get());
//double[] normalizedLog10Posteriors = MathUtils.normalizeFromLog10(log10AlleleFrequencyPosteriors.get(), true);
double forwardLog10PofNull = log10AlleleFrequencyPosteriors.get()[0];
double forwardLog10PofF = MathUtils.log10sumLog10(log10AlleleFrequencyPosteriors.get(), 1);
@ -400,7 +400,7 @@ public class UnifiedGenotyperEngine {
// the reverse lod
VariantContext vcReverse = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.REVERSE, vc.getAlternateAllele(0), false, model);
clearAFarray(log10AlleleFrequencyPosteriors.get());
afcm.get().getLog10PNonRef(tracker, refContext, vcReverse.getGenotypes(), vc.getAlleles(), getAlleleFrequencyPriors(model), log10AlleleFrequencyPosteriors.get());
afcm.get().getLog10PNonRef(vcReverse.getGenotypes(), vc.getAlleles(), getAlleleFrequencyPriors(model), log10AlleleFrequencyPosteriors.get());
//normalizedLog10Posteriors = MathUtils.normalizeFromLog10(log10AlleleFrequencyPosteriors.get(), true);
double reverseLog10PofNull = log10AlleleFrequencyPosteriors.get()[0];
double reverseLog10PofF = MathUtils.log10sumLog10(log10AlleleFrequencyPosteriors.get(), 1);
@ -447,6 +447,78 @@ public class UnifiedGenotyperEngine {
return new VariantCallContext(vcCall, confidentlyCalled(phredScaledConfidence, PofF));
}
// A barebones entry point to the exact model when there is no tracker or stratified contexts available -- only GLs
public VariantCallContext calculateGenotypes(final VariantContext vc, final GenomeLoc loc, final GenotypeLikelihoodsCalculationModel.Model model) {
// initialize the data for this thread if that hasn't been done yet
if ( afcm.get() == null ) {
log10AlleleFrequencyPosteriors.set(new double[N+1]);
afcm.set(getAlleleFrequencyCalculationObject(N, logger, verboseWriter, UAC));
}
// estimate our confidence in a reference call and return
if ( vc.getNSamples() == 0 )
return null;
// 'zero' out the AFs (so that we don't have to worry if not all samples have reads at this position)
clearAFarray(log10AlleleFrequencyPosteriors.get());
afcm.get().getLog10PNonRef(vc.getGenotypes(), vc.getAlleles(), getAlleleFrequencyPriors(model), log10AlleleFrequencyPosteriors.get());
// find the most likely frequency
int bestAFguess = MathUtils.maxElementIndex(log10AlleleFrequencyPosteriors.get());
// calculate p(f>0)
double[] normalizedPosteriors = MathUtils.normalizeFromLog10(log10AlleleFrequencyPosteriors.get());
double sum = 0.0;
for (int i = 1; i <= N; i++)
sum += normalizedPosteriors[i];
double PofF = Math.min(sum, 1.0); // deal with precision errors
double phredScaledConfidence;
if ( bestAFguess != 0 || UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
phredScaledConfidence = QualityUtils.phredScaleErrorRate(normalizedPosteriors[0]);
if ( Double.isInfinite(phredScaledConfidence) )
phredScaledConfidence = -10.0 * log10AlleleFrequencyPosteriors.get()[0];
} else {
phredScaledConfidence = QualityUtils.phredScaleErrorRate(PofF);
if ( Double.isInfinite(phredScaledConfidence) ) {
sum = 0.0;
for (int i = 1; i <= N; i++) {
if ( log10AlleleFrequencyPosteriors.get()[i] == AlleleFrequencyCalculationModel.VALUE_NOT_CALCULATED )
break;
sum += log10AlleleFrequencyPosteriors.get()[i];
}
phredScaledConfidence = (MathUtils.compareDoubles(sum, 0.0) == 0 ? 0 : -10.0 * sum);
}
}
// return a null call if we don't pass the confidence cutoff or the most likely allele frequency is zero
if ( UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES && !passesEmitThreshold(phredScaledConfidence, bestAFguess) ) {
// technically, at this point our confidence in a reference call isn't accurately estimated
// because it didn't take into account samples with no data, so let's get a better estimate
return null;
}
// create the genotypes
Map<String, Genotype> genotypes = afcm.get().assignGenotypes(vc, log10AlleleFrequencyPosteriors.get(), bestAFguess);
// *** note that calculating strand bias involves overwriting data structures, so we do that last
HashMap<String, Object> attributes = new HashMap<String, Object>();
int endLoc = calculateEndPos(vc.getAlleles(), vc.getReference(), loc);
Set<Allele> myAlleles = new HashSet<Allele>(vc.getAlleles());
// strip out the alternate allele if it's a ref call
if ( bestAFguess == 0 && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY ) {
myAlleles = new HashSet<Allele>(1);
myAlleles.add(vc.getReference());
}
VariantContext vcCall = new VariantContext("UG_call", loc.getContig(), loc.getStart(), endLoc,
myAlleles, genotypes, phredScaledConfidence/10.0, passesCallThreshold(phredScaledConfidence) ? null : filter, attributes, vc.getReferenceBaseForIndel());
return new VariantCallContext(vcCall, confidentlyCalled(phredScaledConfidence, PofF));
}
private int calculateEndPos(Collection<Allele> alleles, Allele refAllele, GenomeLoc loc) {
// TODO - temp fix until we can deal with extended events properly
// for indels, stop location is one more than ref allele length

282
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
View File

@ -32,11 +32,17 @@ import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import java.io.File;
import java.io.FileWriter;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.LinkedHashMap;
@ -45,9 +51,6 @@ import java.util.LinkedHashMap;
public class PairHMMIndelErrorModel {
public static final int BASE_QUAL_THRESHOLD = 20;
private final double logGapOpenProbability;
private final double logGapContinuationProbability;
private boolean DEBUG = false;
private boolean bandedLikelihoods = false;
@ -89,8 +92,6 @@ public class PairHMMIndelErrorModel {
}
public PairHMMIndelErrorModel(double indelGOP, double indelGCP, boolean deb, boolean bandedLikelihoods) {
this.logGapOpenProbability = -indelGOP/10.0; // QUAL to log prob
this.logGapContinuationProbability = -indelGCP/10.0; // QUAL to log prob
this.DEBUG = deb;
this.bandedLikelihoods = bandedLikelihoods;
@ -98,13 +99,14 @@ public class PairHMMIndelErrorModel {
this.GAP_CONT_PROB_TABLE = new double[MAX_HRUN_GAP_IDX];
this.GAP_OPEN_PROB_TABLE = new double[MAX_HRUN_GAP_IDX];
double gop = -indelGOP/10.0;
double gcp = -indelGCP/10.0;
for (int i = 0; i < START_HRUN_GAP_IDX; i++) {
GAP_OPEN_PROB_TABLE[i] = logGapOpenProbability;
GAP_CONT_PROB_TABLE[i] = logGapContinuationProbability;
GAP_OPEN_PROB_TABLE[i] = gop;
GAP_CONT_PROB_TABLE[i] = gcp;
}
double gop = logGapOpenProbability;
double gcp = logGapContinuationProbability;
double step = GAP_PENALTY_HRUN_STEP/10.0;
double maxGOP = -MIN_GAP_OPEN_PENALTY/10.0; // phred to log prob
@ -185,60 +187,57 @@ public class PairHMMIndelErrorModel {
}
private double computeReadLikelihoodGivenHaplotypeAffineGaps(byte[] haplotypeBases, byte[] readBases, byte[] readQuals,
double[] currentGOP, double[] currentGCP, int eventLength) {
double[] currentGOP, double[] currentGCP, int indToStart,
double[][] matchMetricArray, double[][] XMetricArray, double[][] YMetricArray) {
final int X_METRIC_LENGTH = readBases.length+1;
final int Y_METRIC_LENGTH = haplotypeBases.length+1;
// initialize path metric and traceback memories for likelihood computation
final double[][] matchMetricArray = new double[X_METRIC_LENGTH][Y_METRIC_LENGTH];
final double[][] XMetricArray = new double[X_METRIC_LENGTH][Y_METRIC_LENGTH];
final double[][] YMetricArray = new double[X_METRIC_LENGTH][Y_METRIC_LENGTH];
if (indToStart == 0) {
// default initialization for all arrays
final double DIAG_TOL = 20; // means that max - min element in diags have to be > this number for banding to take effect.
// default initialization for all arrays
for (int i=0; i < X_METRIC_LENGTH; i++) {
Arrays.fill(matchMetricArray[i],Double.NEGATIVE_INFINITY);
Arrays.fill(YMetricArray[i],Double.NEGATIVE_INFINITY);
Arrays.fill(XMetricArray[i],Double.NEGATIVE_INFINITY);
}
for (int i=1; i < X_METRIC_LENGTH; i++) {
//initialize first column
XMetricArray[i][0] = END_GAP_COST*(i);
}
for (int j=1; j < Y_METRIC_LENGTH; j++) {
// initialize first row
YMetricArray[0][j] = END_GAP_COST*(j);
}
matchMetricArray[0][0]= END_GAP_COST;//Double.NEGATIVE_INFINITY;
XMetricArray[0][0]= YMetricArray[0][0] = 0;
final int numDiags = X_METRIC_LENGTH + Y_METRIC_LENGTH -1;
final int elemsInDiag = Math.min(X_METRIC_LENGTH, Y_METRIC_LENGTH);
int idxWithMaxElement = 0;
double maxElementInDiag = Double.NEGATIVE_INFINITY;
for (int diag=0; diag < numDiags; diag++) {
// compute default I and J start positions at edge of diagonals
int indI = 0;
int indJ = diag;
if (diag >= Y_METRIC_LENGTH ) {
indI = diag-(Y_METRIC_LENGTH-1);
indJ = Y_METRIC_LENGTH-1;
for (int i=0; i < X_METRIC_LENGTH; i++) {
Arrays.fill(matchMetricArray[i],Double.NEGATIVE_INFINITY);
Arrays.fill(YMetricArray[i],Double.NEGATIVE_INFINITY);
Arrays.fill(XMetricArray[i],Double.NEGATIVE_INFINITY);
}
// first pass: from max element to edge
int idxLow = bandedLikelihoods? idxWithMaxElement : 0;
for (int i=1; i < X_METRIC_LENGTH; i++) {
//initialize first column
XMetricArray[i][0] = END_GAP_COST*(i);
}
// reset diag max value before starting
if (bandedLikelihoods) {
maxElementInDiag = Double.NEGATIVE_INFINITY;
for (int j=1; j < Y_METRIC_LENGTH; j++) {
// initialize first row
YMetricArray[0][j] = END_GAP_COST*(j);
}
matchMetricArray[0][0]= END_GAP_COST;//Double.NEGATIVE_INFINITY;
XMetricArray[0][0]= YMetricArray[0][0] = 0;
}
if (bandedLikelihoods) {
final double DIAG_TOL = 20; // means that max - min element in diags have to be > this number for banding to take effect.
final int numDiags = X_METRIC_LENGTH + Y_METRIC_LENGTH -1;
final int elemsInDiag = Math.min(X_METRIC_LENGTH, Y_METRIC_LENGTH);
int idxWithMaxElement = 0;
for (int diag=indToStart; diag < numDiags; diag++) {
// compute default I and J start positions at edge of diagonals
int indI = 0;
int indJ = diag;
if (diag >= Y_METRIC_LENGTH ) {
indI = diag-(Y_METRIC_LENGTH-1);
indJ = Y_METRIC_LENGTH-1;
}
// first pass: from max element to edge
int idxLow = idxWithMaxElement;
// reset diag max value before starting
double maxElementInDiag = Double.NEGATIVE_INFINITY;
// set indI, indJ to correct values
indI += idxLow;
indJ -= idxLow;
@ -248,46 +247,10 @@ public class PairHMMIndelErrorModel {
indJ++;
}
}
for (int el = idxLow; el < elemsInDiag; el++) {
updateCell(indI, indJ, X_METRIC_LENGTH, Y_METRIC_LENGTH, readBases, readQuals, haplotypeBases,
currentGOP, currentGCP, matchMetricArray, XMetricArray, YMetricArray);
// update max in diagonal
if (bandedLikelihoods) {
final double bestMetric = MathUtils.max(matchMetricArray[indI][indJ], XMetricArray[indI][indJ], YMetricArray[indI][indJ]);
// check if we've fallen off diagonal value by threshold
if (bestMetric > maxElementInDiag) {
maxElementInDiag = bestMetric;
idxWithMaxElement = el;
}
else if (bestMetric < maxElementInDiag - DIAG_TOL)
break; // done w/current diagonal
}
indI++;
if (indI >=X_METRIC_LENGTH )
break;
indJ--;
if (indJ <= 0)
break;
}
if (bandedLikelihoods && idxLow > 0) {
// now do second part in opposite direction
indI = 0;
indJ = diag;
if (diag >= Y_METRIC_LENGTH ) {
indI = diag-(Y_METRIC_LENGTH-1);
indJ = Y_METRIC_LENGTH-1;
}
indI += idxLow-1;
indJ -= idxLow-1;
for (int el = idxLow-1; el >= 0; el--) {
for (int el = idxLow; el < elemsInDiag; el++) {
updateCell(indI, indJ, X_METRIC_LENGTH, Y_METRIC_LENGTH, readBases, readQuals, haplotypeBases,
currentGOP, currentGCP, matchMetricArray, XMetricArray, YMetricArray);
currentGOP, currentGCP, matchMetricArray, XMetricArray, YMetricArray);
// update max in diagonal
final double bestMetric = MathUtils.max(matchMetricArray[indI][indJ], XMetricArray[indI][indJ], YMetricArray[indI][indJ]);
@ -296,34 +259,81 @@ public class PairHMMIndelErrorModel {
maxElementInDiag = bestMetric;
idxWithMaxElement = el;
}
else if (bestMetric < maxElementInDiag - DIAG_TOL)
else if (bestMetric < maxElementInDiag - DIAG_TOL && idxWithMaxElement > 0)
break; // done w/current diagonal
indJ++;
if (indJ >= Y_METRIC_LENGTH )
indI++;
if (indI >=X_METRIC_LENGTH )
break;
indI--;
if (indI <= 0)
indJ--;
if (indJ <= 0)
break;
}
if (idxLow > 0) {
// now do second part in opposite direction
indI = 0;
indJ = diag;
if (diag >= Y_METRIC_LENGTH ) {
indI = diag-(Y_METRIC_LENGTH-1);
indJ = Y_METRIC_LENGTH-1;
}
indI += idxLow-1;
indJ -= idxLow-1;
for (int el = idxLow-1; el >= 0; el--) {
updateCell(indI, indJ, X_METRIC_LENGTH, Y_METRIC_LENGTH, readBases, readQuals, haplotypeBases,
currentGOP, currentGCP, matchMetricArray, XMetricArray, YMetricArray);
// update max in diagonal
final double bestMetric = MathUtils.max(matchMetricArray[indI][indJ], XMetricArray[indI][indJ], YMetricArray[indI][indJ]);
// check if we've fallen off diagonal value by threshold
if (bestMetric > maxElementInDiag) {
maxElementInDiag = bestMetric;
idxWithMaxElement = el;
}
else if (bestMetric < maxElementInDiag - DIAG_TOL)
break; // done w/current diagonal
indJ++;
if (indJ >= Y_METRIC_LENGTH )
break;
indI--;
if (indI <= 0)
break;
}
}
// if (DEBUG)
// System.out.format("Max:%4.1f el:%d\n",maxElementInDiag, idxWithMaxElement);
}
// if (DEBUG)
// System.out.format("Max:%4.1f el:%d\n",maxElementInDiag, idxWithMaxElement);
}
else {
// simplified rectangular version of update loop
for (int indI=1; indI < X_METRIC_LENGTH; indI++) {
for (int indJ=indToStart+1; indJ < Y_METRIC_LENGTH; indJ++) {
updateCell(indI, indJ, X_METRIC_LENGTH, Y_METRIC_LENGTH, readBases, readQuals, haplotypeBases,
currentGOP, currentGCP, matchMetricArray, XMetricArray, YMetricArray);
}
}
}
final int bestI = X_METRIC_LENGTH - 1, bestJ = Y_METRIC_LENGTH - 1;
final double bestMetric = MathUtils.softMax(matchMetricArray[bestI][bestJ],
XMetricArray[bestI][bestJ],
YMetricArray[bestI][bestJ]);
/*
/*
if (DEBUG) {
PrintStream outx, outy, outm, outs;
double[][] sumMetrics = new double[X_METRIC_LENGTH][Y_METRIC_LENGTH];
try {
outx = new PrintStream("../../UGOptim/datax.txt");
outy = new PrintStream("../../UGOptim/datay.txt");
outm = new PrintStream("../../UGOptim/datam.txt");
outs = new PrintStream("../../UGOptim/datas.txt");
outx = new PrintStream("datax.txt");
outy = new PrintStream("datay.txt");
outm = new PrintStream("datam.txt");
outs = new PrintStream("datas.txt");
double metrics[] = new double[3];
for (int indI=0; indI < X_METRIC_LENGTH; indI++) {
for (int indJ=0; indJ < Y_METRIC_LENGTH; indJ++) {
@ -393,7 +403,7 @@ public class PairHMMIndelErrorModel {
for (PileupElement p: pileup) {
// > 1 when the read is a consensus read representing multiple independent observations
final boolean isReduced = ReadUtils.isReducedRead(p.getRead());
final boolean isReduced = p.isReducedRead();
readCounts[readIdx] = isReduced ? p.getReducedCount() : 1;
// check if we've already computed likelihoods for this pileup element (i.e. for this read at this location)
@ -414,8 +424,6 @@ public class PairHMMIndelErrorModel {
continue;
}
double[] recalQuals = null;
// get bases of candidate haplotypes that overlap with reads
final int trailingBases = 3;
@ -534,6 +542,12 @@ public class PairHMMIndelErrorModel {
unclippedReadBases.length-numEndClippedBases);
int j=0;
// initialize path metric and traceback memories for likelihood computation
double[][] matchMetricArray = null, XMetricArray = null, YMetricArray = null;
byte[] previousHaplotypeSeen = null;
double[] previousGOP = null;
int startIdx;
for (Allele a: haplotypeMap.keySet()) {
@ -551,11 +565,37 @@ public class PairHMMIndelErrorModel {
byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBasesAsBytes(),
(int)indStart, (int)indStop);
double readLikelihood;
if (matchMetricArray == null) {
final int X_METRIC_LENGTH = readBases.length+1;
final int Y_METRIC_LENGTH = haplotypeBases.length+1;
matchMetricArray = new double[X_METRIC_LENGTH][Y_METRIC_LENGTH];
XMetricArray = new double[X_METRIC_LENGTH][Y_METRIC_LENGTH];
YMetricArray = new double[X_METRIC_LENGTH][Y_METRIC_LENGTH];
}
final double[] currentContextGOP = Arrays.copyOfRange(gapOpenProbabilityMap.get(a), (int)indStart, (int)indStop);
final double[] currentContextGCP = Arrays.copyOfRange(gapContProbabilityMap.get(a), (int)indStart, (int)indStop);
final double readLikelihood = computeReadLikelihoodGivenHaplotypeAffineGaps(haplotypeBases, readBases, readQuals,
currentContextGOP, currentContextGCP, eventLength);
if (previousHaplotypeSeen == null)
startIdx = 0;
else {
int s1 = computeFirstDifferingPosition(haplotypeBases, previousHaplotypeSeen);
int s2 = computeFirstDifferingPosition(currentContextGOP, previousGOP);
startIdx = Math.min(s1,s2);
}
previousHaplotypeSeen = haplotypeBases.clone();
previousGOP = currentContextGOP.clone();
readLikelihood = computeReadLikelihoodGivenHaplotypeAffineGaps(haplotypeBases, readBases, readQuals,
currentContextGOP, currentContextGCP, startIdx, matchMetricArray, XMetricArray, YMetricArray);
if (DEBUG) {
System.out.println("H:"+new String(haplotypeBases));
System.out.println("R:"+new String(readBases));
System.out.format("L:%4.2f\n",readLikelihood);
System.out.format("StPos:%d\n", startIdx);
}
readEl.put(a,readLikelihood);
readLikelihoods[readIdx][j++] = readLikelihood;
}
@ -579,6 +619,28 @@ public class PairHMMIndelErrorModel {
return getHaplotypeLikelihoods(numHaplotypes, readCounts, readLikelihoods);
}
private int computeFirstDifferingPosition(byte[] b1, byte[] b2) {
if (b1.length != b2.length)
return 0; // sanity check
for (int i=0; i < b1.length; i++ ){
if ( b1[i]!= b2[i])
return i;
}
return 0; // sanity check
}
private int computeFirstDifferingPosition(double[] b1, double[] b2) {
if (b1.length != b2.length)
return 0; // sanity check
for (int i=0; i < b1.length; i++ ){
if ( b1[i]!= b2[i])
return i;
}
return 0; // sanity check
}
private final static double[] getHaplotypeLikelihoods(final int numHaplotypes, final int readCounts[], final double readLikelihoods[][]) {
final double[][] haplotypeLikehoodMatrix = new double[numHaplotypes][numHaplotypes];

130
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
View File

@ -2,9 +2,12 @@ package org.broadinstitute.sting.gatk.walkers.recalibration;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.NGSPlatform;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.util.Arrays;
import java.util.EnumSet;
import java.util.List;
/*
@ -46,6 +49,9 @@ import java.util.List;
*/
public class CycleCovariate implements StandardCovariate {
private final static EnumSet<NGSPlatform> DISCRETE_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.ILLUMINA, NGSPlatform.SOLID, NGSPlatform.PACBIO, NGSPlatform.COMPLETE_GENOMICS);
private final static EnumSet<NGSPlatform> FLOW_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.LS454, NGSPlatform.ION_TORRENT);
// Initialize any member variables using the command-line arguments passed to the walkers
public void initialize( final RecalibrationArgumentCollection RAC ) {
if( RAC.DEFAULT_PLATFORM != null ) {
@ -58,122 +64,6 @@ public class CycleCovariate implements StandardCovariate {
}
}
/*
// Used to pick out the covariate's value from attributes of the read
public final Comparable getValue( final SAMRecord read, final int offset ) {
int cycle = 1;
//-----------------------------
// ILLUMINA and SOLID
//-----------------------------
if( read.getReadGroup().getPlatform().equalsIgnoreCase( "ILLUMINA" ) || read.getReadGroup().getPlatform().equalsIgnoreCase( "SLX" ) || // Some bams have "illumina" and others have "SLX"
read.getReadGroup().getPlatform().equalsIgnoreCase( "SOLID" ) || read.getReadGroup().getPlatform().equalsIgnoreCase( "ABI_SOLID" )) { // Some bams have "solid" and others have "ABI_SOLID"
cycle = offset + 1;
if( read.getReadNegativeStrandFlag() ) {
cycle = read.getReadLength() - offset;
}
}
//-----------------------------
// 454
//-----------------------------
else if( read.getReadGroup().getPlatform().contains( "454" ) ) { // Some bams have "LS454" and others have just "454"
final byte[] bases = read.getReadBases();
// BUGBUG: Consider looking at degradation of base quality scores in homopolymer runs to detect when the cycle incremented even though the nucleotide didn't change
// For example, AAAAAAA was probably read in two flow cycles but here we count it as one
if( !read.getReadNegativeStrandFlag() ) { // Forward direction
int iii = 0;
while( iii <= offset )
{
while( iii <= offset && bases[iii] == (byte)'T' ) { iii++; }
while( iii <= offset && bases[iii] == (byte)'A' ) { iii++; }
while( iii <= offset && bases[iii] == (byte)'C' ) { iii++; }
while( iii <= offset && bases[iii] == (byte)'G' ) { iii++; }
if( iii <= offset ) { cycle++; }
if( iii <= offset && !BaseUtils.isRegularBase(bases[iii]) ) { iii++; }
}
} else { // Negative direction
int iii = bases.length-1;
while( iii >= offset )
{
while( iii >= offset && bases[iii] == (byte)'T' ) { iii--; }
while( iii >= offset && bases[iii] == (byte)'A' ) { iii--; }
while( iii >= offset && bases[iii] == (byte)'C' ) { iii--; }
while( iii >= offset && bases[iii] == (byte)'G' ) { iii--; }
if( iii >= offset ) { cycle++; }
if( iii >= offset && !BaseUtils.isRegularBase(bases[iii]) ) { iii--; }
}
}
}
//-----------------------------
// SOLID (unused), only to be used in conjunction with PrimerRoundCovariate
//-----------------------------
//else if( read.getReadGroup().getPlatform().equalsIgnoreCase( "SOLID" ) ) {
// // The ligation cycle according to http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_057511.pdf
// int pos = offset + 1;
// if( read.getReadNegativeStrandFlag() ) {
// pos = read.getReadLength() - offset;
// }
// cycle = pos / 5; // integer division
//}
//-----------------------------
// UNRECOGNIZED PLATFORM
//-----------------------------
else { // Platform is unrecognized so revert to the default platform but warn the user first
if( defaultPlatform != null) { // The user set a default platform
if( !warnedUserBadPlatform ) {
Utils.warnUser( "Platform string (" + read.getReadGroup().getPlatform() + ") unrecognized in CycleCovariate. " +
"Defaulting to platform = " + defaultPlatform + "." );
}
warnedUserBadPlatform = true;
read.getReadGroup().setPlatform( defaultPlatform );
return getValue( read, offset ); // A recursive call
} else { // The user did not set a default platform
throw new StingException( "Platform string (" + read.getReadGroup().getPlatform() + ") unrecognized in CycleCovariate. " +
"No default platform specified. Users must set the default platform using the --default_platform <String> argument." );
}
}
// Differentiate between first and second of pair.
// The sequencing machine cycle keeps incrementing for the second read in a pair. So it is possible for a read group
// to have an error affecting quality at a particular cycle on the first of pair which carries over to the second of pair.
// Therefore the cycle covariate must differentiate between first and second of pair reads.
// This effect can not be corrected by pulling out the first of pair and second of pair flags into a separate covariate because
// the current sequential model would consider the effects independently instead of jointly.
if( read.getReadPairedFlag() && read.getSecondOfPairFlag() ) {
cycle *= -1;
}
return cycle;
}
*/
// todo -- this should be put into a common place in the code base
private static List<String> ILLUMINA_NAMES = Arrays.asList("ILLUMINA", "SLX", "SOLEXA");
private static List<String> SOLID_NAMES = Arrays.asList("SOLID");
private static List<String> LS454_NAMES = Arrays.asList("454");
private static List<String> COMPLETE_GENOMICS_NAMES = Arrays.asList("COMPLETE");
private static List<String> PACBIO_NAMES = Arrays.asList("PACBIO");
private static List<String> ION_TORRENT_NAMES = Arrays.asList("IONTORRENT");
private static boolean isPlatform(SAMRecord read, List<String> names) {
String pl = read.getReadGroup().getPlatform().toUpperCase();
for ( String name : names )
if ( pl.contains( name ) )
return true;
return false;
}
// Used to pick out the covariate's value from attributes of the read
public void getValues(SAMRecord read, Comparable[] comparable) {
@ -181,7 +71,8 @@ public class CycleCovariate implements StandardCovariate {
// Illumina, Solid, PacBio, and Complete Genomics
//-----------------------------
if( isPlatform(read, ILLUMINA_NAMES) || isPlatform(read, SOLID_NAMES) || isPlatform(read, PACBIO_NAMES) || isPlatform(read, COMPLETE_GENOMICS_NAMES) ) {
final NGSPlatform ngsPlatform = ((GATKSAMRecord)read).getNGSPlatform();
if( DISCRETE_CYCLE_PLATFORMS.contains(ngsPlatform) ) {
final int init;
final int increment;
if( !read.getReadNegativeStrandFlag() ) {
@ -227,8 +118,7 @@ public class CycleCovariate implements StandardCovariate {
//-----------------------------
// 454 and Ion Torrent
//-----------------------------
else if ( isPlatform(read, LS454_NAMES) || isPlatform(read, ION_TORRENT_NAMES)) { // Some bams have "LS454" and others have just "454"
else if( FLOW_CYCLE_PLATFORMS.contains(ngsPlatform) ) {
final int readLength = read.getReadLength();
final byte[] bases = read.getReadBases();
@ -273,8 +163,6 @@ public class CycleCovariate implements StandardCovariate {
else {
throw new IllegalStateException("This method hasn't been implemented yet for " + read.getReadGroup().getPlatform());
}
}
// Used to get the covariate's value from input csv file in TableRecalibrationWalker

8
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
View File

@ -35,6 +35,7 @@ import org.broadinstitute.sting.utils.collections.NestedHashMap;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.util.ArrayList;
@ -228,8 +229,7 @@ public class RecalDataManager {
* @param RAC The list of shared command line arguments
*/
public static void parseSAMRecord( final SAMRecord read, final RecalibrationArgumentCollection RAC ) {
SAMReadGroupRecord readGroup = read.getReadGroup();
GATKSAMReadGroupRecord readGroup = ((GATKSAMRecord)read).getReadGroup();
// If there are no read groups we have to default to something, and that something could be specified by the user using command line arguments
if( readGroup == null ) {
@ -241,7 +241,7 @@ public class RecalDataManager {
warnUserNullReadGroup = true;
}
// There is no readGroup so defaulting to these values
readGroup = new SAMReadGroupRecord( RAC.DEFAULT_READ_GROUP );
readGroup = new GATKSAMReadGroupRecord( RAC.DEFAULT_READ_GROUP );
readGroup.setPlatform( RAC.DEFAULT_PLATFORM );
((GATKSAMRecord)read).setReadGroup( readGroup );
} else {
@ -251,7 +251,7 @@ public class RecalDataManager {
if( RAC.FORCE_READ_GROUP != null && !readGroup.getReadGroupId().equals(RAC.FORCE_READ_GROUP) ) { // Collapse all the read groups into a single common String provided by the user
final String oldPlatform = readGroup.getPlatform();
readGroup = new SAMReadGroupRecord( RAC.FORCE_READ_GROUP );
readGroup = new GATKSAMReadGroupRecord( RAC.FORCE_READ_GROUP );
readGroup.setPlatform( oldPlatform );
((GATKSAMRecord)read).setReadGroup( readGroup );
}

52
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java 100644
View File

@ -0,0 +1,52 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.ArrayList;
import java.util.List;
/**
* Stratifies the eval RODs by the indel size
*
* Indel sizes are stratified from sizes -100 to +100. Sizes greater than this are lumped in the +/- 100 bin
* This stratification ignores multi-allelic indels (whose size is not defined uniquely)
*/
public class IndelSize extends VariantStratifier {
static final int MAX_INDEL_SIZE = 100;
@Override
public void initialize() {
states = new ArrayList<String>();
for( int a=-MAX_INDEL_SIZE; a <=MAX_INDEL_SIZE; a++ ) {
states.add(String.format("%d", a));
}
}
public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
ArrayList<String> relevantStates = new ArrayList<String>();
if (eval != null && eval.isIndel() && eval.isBiallelic()) {
try {
int eventLength = 0;
if ( eval.isSimpleInsertion() ) {
eventLength = eval.getAlternateAllele(0).length();
} else if ( eval.isSimpleDeletion() ) {
eventLength = -eval.getReference().length();
}
if (eventLength > MAX_INDEL_SIZE)
eventLength = MAX_INDEL_SIZE;
else if (eventLength < -MAX_INDEL_SIZE)
eventLength = -MAX_INDEL_SIZE;
relevantStates.add(String.format("%d",eventLength));
} catch (Exception e) {
return relevantStates;
}
}
return relevantStates;
}
}

108
public/java/src/org/broadinstitute/sting/utils/NGSPlatform.java 100644
View File

@ -0,0 +1,108 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
/**
* A canonical, master list of the standard NGS platforms. These values
* can be obtained (efficiently) from a GATKSAMRecord object with the
* getNGSPlatform method.
*
* @author Mark DePristo
* @since 2011
*/
public enum NGSPlatform {
ILLUMINA("ILLUMINA", "SLX", "SOLEXA"),
SOLID("SOLID"),
LS454("454"),
COMPLETE_GENOMICS("COMPLETE"),
PACBIO("PACBIO"),
ION_TORRENT("IONTORRENT"),
UNKNOWN("UNKNOWN");
/**
* Array of the prefix names in a BAM file for each of the platforms.
*/
private final String[] BAM_PL_NAMES;
NGSPlatform(final String... BAM_PL_NAMES) {
for ( int i = 0; i < BAM_PL_NAMES.length; i++ )
BAM_PL_NAMES[i] = BAM_PL_NAMES[i].toUpperCase();
this.BAM_PL_NAMES = BAM_PL_NAMES;
}
/**
* Returns a representative PL string for this platform
* @return
*/
public final String getDefaultPlatform() {
return BAM_PL_NAMES[0];
}
/**
* Convenience constructor -- calculates the NGSPlatfrom from a SAMRecord.
* Note you should not use this function if you have a GATKSAMRecord -- use the
* accessor method instead.
*
* @param read
* @return an NGSPlatform object matching the PL field of the header, of UNKNOWN if there was no match
*/
public static final NGSPlatform fromRead(SAMRecord read) {
return fromReadGroup(read.getReadGroup());
}
/**
* Returns the NGSPlatform corresponding to the PL tag in the read group
* @param rg
* @return an NGSPlatform object matching the PL field of the header, of UNKNOWN if there was no match
*/
public static final NGSPlatform fromReadGroup(SAMReadGroupRecord rg) {
return fromReadGroupPL(rg.getPlatform());
}
/**
* Returns the NGSPlatform corresponding to the PL tag in the read group
* @param plFromRG -- the PL field (or equivalent) in a ReadGroup object
* @return an NGSPlatform object matching the PL field of the header, of UNKNOWN if there was no match
*/
public static final NGSPlatform fromReadGroupPL(final String plFromRG) {
if ( plFromRG == null ) return UNKNOWN;
// todo -- algorithm could be implemented more efficiently, as the list of all
// todo -- names is known upfront, so a decision tree could be used to identify
// todo -- a prefix common to PL
final String pl = plFromRG.toUpperCase();
for ( final NGSPlatform ngsPlatform : NGSPlatform.values() ) {
for ( final String bamPLName : ngsPlatform.BAM_PL_NAMES ) {
if ( pl.contains(bamPLName) )
return ngsPlatform;
}
}
return UNKNOWN;
}
}

129
public/java/src/org/broadinstitute/sting/utils/R/RScriptExecutor.java
View File

@ -25,35 +25,35 @@
package org.broadinstitute.sting.utils.R;
import org.apache.commons.io.FileUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.commandline.Advanced;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.gatk.walkers.recalibration.Covariate;
import org.broadinstitute.sting.utils.PathUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.io.IOUtils;
import org.broadinstitute.sting.utils.io.Resource;
import org.broadinstitute.sting.utils.runtime.ProcessController;
import org.broadinstitute.sting.utils.runtime.ProcessSettings;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
/**
* Generic service for executing RScripts in the GATK directory
*
* @author Your Name
* @since Date created
* Generic service for executing RScripts
*/
public class RScriptExecutor {
/**
* our log
*/
protected static Logger logger = Logger.getLogger(RScriptExecutor.class);
private static Logger logger = Logger.getLogger(RScriptExecutor.class);
public static class RScriptArgumentCollection {
@Advanced
@Argument(fullName = "path_to_Rscript", shortName = "Rscript", doc = "The path to your implementation of Rscript. For Broad users this is maybe /broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.12.0/bin/Rscript", required = false)
@Argument(fullName = "path_to_Rscript", shortName = "Rscript", doc = "The path to your implementation of Rscript. Defaults Rscript meaning to use the first available on the environment PATH. For Broad users should 'use R-2.12' or later.", required = false)
public String PATH_TO_RSCRIPT = "Rscript";
@Advanced
@ -62,40 +62,119 @@ public class RScriptExecutor {
public RScriptArgumentCollection() {}
/** For testing and convenience */
/* For testing and convenience */
public RScriptArgumentCollection(final String PATH_TO_RSCRIPT, final List<String> PATH_TO_RESOURCES) {
this.PATH_TO_RSCRIPT = PATH_TO_RSCRIPT;
this.PATH_TO_RESOURCES = PATH_TO_RESOURCES;
}
}
final RScriptArgumentCollection myArgs;
final boolean exceptOnError;
private final RScriptArgumentCollection myArgs;
private final boolean exceptOnError;
private final List<RScriptLibrary> libraries = new ArrayList<RScriptLibrary>();
private final List<Resource> scriptResources = new ArrayList<Resource>();
private final List<File> scriptFiles = new ArrayList<File>();
private final List<String> args = new ArrayList<String>();
public RScriptExecutor(final RScriptArgumentCollection myArgs, final boolean exceptOnError) {
this.myArgs = myArgs;
this.exceptOnError = exceptOnError;
}
public void callRScripts(String scriptName, Object... scriptArgs) {
callRScripts(scriptName, Arrays.asList(scriptArgs));
public void addLibrary(RScriptLibrary library) {
this.libraries.add(library);
}
public void callRScripts(String scriptName, List<Object> scriptArgs) {
public void addScript(Resource script) {
this.scriptResources.add(script);
}
public void addScript(File script) {
this.scriptFiles.add(script);
}
/**
* Adds args to the end of the Rscript command line.
* @param args the args.
* @throws NullPointerException if any of the args are null.
*/
public void addArgs(Object... args) {
for (Object arg: args)
this.args.add(arg.toString());
}
public void exec() {
List<File> tempFiles = new ArrayList<File>();
try {
final File pathToScript = findScript(scriptName);
if ( pathToScript == null ) return; // we failed but shouldn't exception out
final String argString = Utils.join(" ", scriptArgs);
final String cmdLine = Utils.join(" ", Arrays.asList(myArgs.PATH_TO_RSCRIPT, pathToScript, argString));
logger.info("Executing RScript: " + cmdLine);
Runtime.getRuntime().exec(cmdLine).waitFor();
} catch (InterruptedException e) {
File tempLibDir = IOUtils.tempDir("R.", ".lib");
tempFiles.add(tempLibDir);
StringBuilder expression = new StringBuilder("tempLibDir = '").append(tempLibDir).append("';");
if (this.libraries.size() > 0) {
List<String> tempLibraryPaths = new ArrayList<String>();
for (RScriptLibrary library: this.libraries) {
File tempLibrary = library.writeTemp();
tempFiles.add(tempLibrary);
tempLibraryPaths.add(tempLibrary.getAbsolutePath());
}
expression.append("install.packages(");
expression.append("pkgs=c('").append(StringUtils.join(tempLibraryPaths, "', '")).append("'), lib=tempLibDir, repos=NULL, type='source', ");
// Install faster by eliminating cruft.
expression.append("INSTALL_opts=c('--no-libs', '--no-data', '--no-help', '--no-demo', '--no-exec')");
expression.append(");");
for (RScriptLibrary library: this.libraries) {
expression.append("require('").append(library.getLibraryName()).append("', lib.loc=tempLibDir);");
}
}
for (Resource script: this.scriptResources) {
File tempScript = IOUtils.writeTempResource(script);
tempFiles.add(tempScript);
expression.append("source('").append(tempScript.getAbsolutePath()).append("');");
}
for (File script: this.scriptFiles) {
expression.append("source('").append(script.getAbsolutePath()).append("');");
}
String[] cmd = new String[this.args.size() + 3];
int i = 0;
cmd[i++] = myArgs.PATH_TO_RSCRIPT;
cmd[i++] = "-e";
cmd[i++] = expression.toString();
for (String arg: this.args)
cmd[i++] = arg;
ProcessSettings processSettings = new ProcessSettings(cmd);
if (logger.isDebugEnabled()) {
processSettings.getStdoutSettings().printStandard(true);
processSettings.getStderrSettings().printStandard(true);
}
ProcessController controller = ProcessController.getThreadLocal();
logger.debug("Executing: " + Utils.join(" ", cmd));
logger.debug("Result: " + controller.exec(processSettings).getExitValue());
} catch (StingException e) {
generateException(e);
} catch (IOException e) {
generateException("Fatal Exception: Perhaps RScript jobs are being spawned too quickly?", e);
} finally {
for (File temp: tempFiles)
FileUtils.deleteQuietly(temp);
}
}
public void callRScripts(String scriptName, Object... scriptArgs) {
final File pathToScript = findScript(scriptName);
if (pathToScript == null) return; // we failed but shouldn't exception out
addScript(pathToScript);
addArgs(scriptArgs);
exec();
}
public File findScript(final String scriptName) {
for ( String pathToResource : myArgs.PATH_TO_RESOURCES ) {
final File f = new File(pathToResource + "/" + scriptName);

59
public/java/src/org/broadinstitute/sting/utils/R/RScriptLibrary.java 100644
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@ -0,0 +1,59 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.R;
import org.broadinstitute.sting.utils.io.IOUtils;
import org.broadinstitute.sting.utils.io.Resource;
import java.io.File;
/**
* Libraries embedded in the StingUtils package.
*/
public enum RScriptLibrary {
GSALIB("gsalib");
private final String name;
private RScriptLibrary(String name) {
this.name = name;
}
public String getLibraryName() {
return this.name;
}
public String getResourcePath() {
return name + ".tar.gz";
}
/**
* Writes the library source code to a temporary tar.gz file and returns the path.
* @return The path to the library source code. The caller must delete the code when done.
*/
public File writeTemp() {
return IOUtils.writeTempResource(new Resource(getResourcePath(), RScriptLibrary.class));
}
}

33
public/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java
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@ -29,6 +29,7 @@ import org.apache.log4j.Logger;
import org.broadinstitute.sting.commandline.ArgumentDefinition;
import org.broadinstitute.sting.commandline.ArgumentDefinitionGroup;
import org.broadinstitute.sting.commandline.ArgumentDefinitions;
import org.broadinstitute.sting.commandline.ArgumentMatchSource;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
@ -47,6 +48,7 @@ public class HelpFormatter {
/**
* Prints the help, given a collection of argument definitions.
* @param applicationDetails Application details
* @param argumentDefinitions Argument definitions for which help should be printed.
*/
public void printHelp( ApplicationDetails applicationDetails, ArgumentDefinitions argumentDefinitions ) {
@ -233,7 +235,7 @@ public class HelpFormatter {
private List<ArgumentDefinitionGroup> prepareArgumentGroups( ArgumentDefinitions argumentDefinitions ) {
// Sort the list of argument definitions according to how they should be shown.
// Put the sorted results into a new cloned data structure.
Comparator definitionComparator = new Comparator<ArgumentDefinition>() {
Comparator<ArgumentDefinition> definitionComparator = new Comparator<ArgumentDefinition>() {
public int compare( ArgumentDefinition lhs, ArgumentDefinition rhs ) {
if( lhs.required && rhs.required ) return 0;
if( lhs.required ) return -1;
@ -242,15 +244,15 @@ public class HelpFormatter {
}
};
List<ArgumentDefinitionGroup> argumentGroups = new ArrayList();
List<ArgumentDefinitionGroup> argumentGroups = new ArrayList<ArgumentDefinitionGroup>();
for( ArgumentDefinitionGroup argumentGroup: argumentDefinitions.getArgumentDefinitionGroups() ) {
List<ArgumentDefinition> sortedDefinitions = new ArrayList( argumentGroup.argumentDefinitions );
List<ArgumentDefinition> sortedDefinitions = new ArrayList<ArgumentDefinition>( argumentGroup.argumentDefinitions );
Collections.sort( sortedDefinitions, definitionComparator );
argumentGroups.add( new ArgumentDefinitionGroup(argumentGroup.groupName,sortedDefinitions) );
}
// Sort the argument groups themselves with main arguments first, followed by plugins sorted in name order.
Comparator groupComparator = new Comparator<ArgumentDefinitionGroup>() {
Comparator<ArgumentDefinitionGroup> groupComparator = new Comparator<ArgumentDefinitionGroup>() {
public int compare( ArgumentDefinitionGroup lhs, ArgumentDefinitionGroup rhs ) {
if( lhs.groupName == null && rhs.groupName == null ) return 0;
if( lhs.groupName == null ) return -1;
@ -271,9 +273,9 @@ public class HelpFormatter {
* Generate a standard header for the logger
*
* @param applicationDetails details of the application to run.
* @param args the command line arguments passed in
* @param parsedArgs the command line arguments passed in
*/
public static void generateHeaderInformation(ApplicationDetails applicationDetails, String[] args) {
public static void generateHeaderInformation(ApplicationDetails applicationDetails, Map<ArgumentMatchSource, List<String>> parsedArgs) {
DateFormat dateFormat = new SimpleDateFormat("yyyy/MM/dd HH:mm:ss");
java.util.Date date = new java.util.Date();
@ -283,11 +285,22 @@ public class HelpFormatter {
logger.info(barrier);
for (String headerLine : applicationDetails.applicationHeader)
logger.info(headerLine);
String output = "";
for (String str : args) {
output = output + str + " ";
logger.debug("Current directory: " + System.getProperty("user.dir"));
for (Map.Entry<ArgumentMatchSource, List<String>> entry: parsedArgs.entrySet()) {
ArgumentMatchSource matchSource = entry.getKey();
final String sourceName;
switch (matchSource.getType()) {
case CommandLine: sourceName = "Program"; break;
case File: sourceName = matchSource.getFile().getPath(); break;
default: throw new RuntimeException("Unexpected argument match source type: " + matchSource.getType());
}
String output = sourceName + " Args:";
for (String str : entry.getValue()) {
output = output + " " + str;
}
logger.info(output);
}
logger.info("Program Args: " + output);
logger.info("Date/Time: " + dateFormat.format(date));
logger.info(barrier);

36
public/java/src/org/broadinstitute/sting/utils/io/FileExtension.java 100644
View File

@ -0,0 +1,36 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.io;
import java.io.File;
public interface FileExtension {
/**
* Returns a clone of the FileExtension with a new path.
* @param path New path.
* @return New FileExtension
*/
public File withPath(String path);
}

54
public/java/src/org/broadinstitute/sting/utils/io/HardThresholdingOutputStream.java 100755
View File

@ -0,0 +1,54 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.io;
import org.apache.commons.io.output.ThresholdingOutputStream;
import java.io.IOException;
/**
* An output stream which stops at the threshold
* instead of potentially triggering early.
*/
public abstract class HardThresholdingOutputStream extends ThresholdingOutputStream {
protected HardThresholdingOutputStream(int threshold) {
super(threshold);
}
@Override
public void write(byte[] b) throws IOException {
write(b, 0, b.length);
}
@Override
public void write(byte[] b, int off, int len) throws IOException {
int remaining = this.getThreshold() - (int)this.getByteCount();
if (!isThresholdExceeded() && len > remaining) {
super.write(b, off, remaining);
super.write(b, off + remaining, len - remaining);
} else {
super.write(b, off, len);
}
}
}

353
public/java/src/org/broadinstitute/sting/utils/io/IOUtils.java 100644
View File

@ -0,0 +1,353 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.io;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.io.LineIterator;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.*;
import java.util.*;
public class IOUtils {
private static Logger logger = Logger.getLogger(IOUtils.class);
/**
* Checks if the temp directory has been setup and throws an exception if they user hasn't set it correctly.
*
* @param tempDir Temporary directory.
*/
public static void checkTempDir(File tempDir) {
String tempDirPath = tempDir.getAbsolutePath();
// Keeps the user from leaving the temp directory as the default, and on Macs from having pluses
// in the path which can cause problems with the Google Reflections library.
// see also: http://benjchristensen.com/2009/09/22/mac-osx-10-6-java-java-io-tmpdir/
if (tempDirPath.startsWith("/var/folders/") || (tempDirPath.equals("/tmp")) || (tempDirPath.equals("/tmp/")))
throw new UserException.BadTmpDir("java.io.tmpdir must be explicitly set");
if (!tempDir.exists() && !tempDir.mkdirs())
throw new UserException.BadTmpDir("Could not create directory: " + tempDir.getAbsolutePath());
}
/**
* Creates a temp directory with the prefix and optional suffix.
*
* @param prefix Prefix for the directory name.
* @param suffix Optional suffix for the directory name.
* @return The created temporary directory.
*/
public static File tempDir(String prefix, String suffix) {
return tempDir(prefix, suffix, null);
}
/**
* Creates a temp directory with the prefix and optional suffix.
*
* @param prefix Prefix for the directory name.
* @param suffix Optional suffix for the directory name.
* @param tempDirParent Parent directory for the temp directory.
* @return The created temporary directory.
*/
public static File tempDir(String prefix, String suffix, File tempDirParent) {
try {
if (tempDirParent == null)
tempDirParent = FileUtils.getTempDirectory();
if (!tempDirParent.exists() && !tempDirParent.mkdirs())
throw new UserException.BadTmpDir("Could not create temp directory: " + tempDirParent);
File temp = File.createTempFile(prefix + "-", suffix, tempDirParent);
if (!temp.delete())
throw new UserException.BadTmpDir("Could not delete sub file: " + temp.getAbsolutePath());
if (!temp.mkdir())
throw new UserException.BadTmpDir("Could not create sub directory: " + temp.getAbsolutePath());
return absolute(temp);
} catch (IOException e) {
throw new UserException.BadTmpDir(e.getMessage());
}
}
/**
* Writes content to a temp file and returns the path to the temporary file.
*
* @param content to write.
* @param prefix Prefix for the temp file.
* @param suffix Suffix for the temp file.
* @param directory Directory for the temp file.
* @return the path to the temp file.
*/
public static File writeTempFile(String content, String prefix, String suffix, File directory) {
try {
File tempFile = absolute(File.createTempFile(prefix, suffix, directory));
FileUtils.writeStringToFile(tempFile, content);
return tempFile;
} catch (IOException e) {
throw new UserException.BadTmpDir(e.getMessage());
}
}
/**
* Waits for NFS to propagate a file creation, imposing a timeout.
*
* Based on Apache Commons IO FileUtils.waitFor()
*
* @param file The file to wait for.
* @param seconds The maximum time in seconds to wait.
* @return true if the file exists
*/
public static boolean waitFor(File file, int seconds) {
return waitFor(Collections.singletonList(file), seconds).isEmpty();
}
/**
* Waits for NFS to propagate a file creation, imposing a timeout.
*
* Based on Apache Commons IO FileUtils.waitFor()
*
* @param files The list of files to wait for.
* @param seconds The maximum time in seconds to wait.
* @return Files that still do not exists at the end of the timeout, or a empty list if all files exists.
*/
public static List<File> waitFor(Collection<File> files, int seconds) {
long timeout = 0;
long tick = 0;
List<File> missingFiles = new ArrayList<File>();
for (File file : files)
if (!file.exists())
missingFiles.add(file);
while (!missingFiles.isEmpty() && timeout <= seconds) {
if (tick >= 10) {
tick = 0;
timeout++;
}
tick++;
try {
Thread.sleep(100);
} catch (InterruptedException ignore) {
}
List<File> newMissingFiles = new ArrayList<File>();
for (File file : missingFiles)
if (!file.exists())
newMissingFiles.add(file);
missingFiles = newMissingFiles;
}
return missingFiles;
}
/**
* Returns the directory at the number of levels deep.
* For example 2 levels of /path/to/dir will return /path/to
*
* @param dir Directory path.
* @param level how many levels deep from the root.
* @return The path to the parent directory that is level-levels deep.
*/
public static File dirLevel(File dir, int level) {
List<File> directories = new ArrayList<File>();
File parentDir = absolute(dir);
while (parentDir != null) {
directories.add(0, parentDir);
parentDir = parentDir.getParentFile();
}
if (directories.size() <= level)
return directories.get(directories.size() - 1);
else
return directories.get(level);
}
/**
* Returns the sub path rooted at the parent.
*
* @param parent The parent directory.
* @param path The sub path to append to the parent, if the path is not absolute.
* @return The absolute path to the file in the parent dir if the path was not absolute, otherwise the original path.
*/
public static File absolute(File parent, String path) {
return absolute(parent, new File(path));
}
/**
* Returns the sub path rooted at the parent.
*
* @param parent The parent directory.
* @param file The sub path to append to the parent, if the path is not absolute.
* @return The absolute path to the file in the parent dir if the path was not absolute, otherwise the original path.
*/
public static File absolute(File parent, File file) {
String newPath;
if (file.isAbsolute())
newPath = absolutePath(file);
else
newPath = absolutePath(new File(parent, file.getPath()));
return replacePath(file, newPath);
}
/**
* A mix of getCanonicalFile and getAbsoluteFile that returns the
* absolute path to the file without deferencing symbolic links.
*
* @param file the file.
* @return the absolute path to the file.
*/
public static File absolute(File file) {
return replacePath(file, absolutePath(file));
}
private static String absolutePath(File file) {
File fileAbs = file.getAbsoluteFile();
LinkedList<String> names = new LinkedList<String>();
while (fileAbs != null) {
String name = fileAbs.getName();
fileAbs = fileAbs.getParentFile();
if (".".equals(name)) {
/* skip */
/* TODO: What do we do for ".."?
} else if (name == "..") {
CentOS tcsh says use getCanonicalFile:
~ $ mkdir -p test1/test2
~ $ ln -s test1/test2 test3
~ $ cd test3/..
~/test1 $
Mac bash says keep going with getAbsoluteFile:
~ $ mkdir -p test1/test2
~ $ ln -s test1/test2 test3
~ $ cd test3/..
~ $
For now, leave it and let the shell figure it out.
*/
} else {
names.add(0, name);
}
}
return ("/" + StringUtils.join(names, "/"));
}
private static File replacePath(File file, String path) {
if (file instanceof FileExtension)
return ((FileExtension)file).withPath(path);
if (!File.class.equals(file.getClass()))
throw new StingException("Sub classes of java.io.File must also implement FileExtension");
return new File(path);
}
/**
* Returns the last lines of the file.
* NOTE: This is only safe to run on smaller files!
*
* @param file File to read.
* @param count Maximum number of lines to return.
* @return The last count lines from file.
* @throws IOException When unable to read the file.
*/
public static List<String> tail(File file, int count) throws IOException {
LinkedList<String> tailLines = new LinkedList<String>();
FileReader reader = new FileReader(file);
try {
LineIterator iterator = org.apache.commons.io.IOUtils.lineIterator(reader);
int lineCount = 0;
while (iterator.hasNext()) {
String line = iterator.nextLine();
lineCount++;
if (lineCount > count)
tailLines.removeFirst();
tailLines.offer(line);
}
} finally {
org.apache.commons.io.IOUtils.closeQuietly(reader);
}
return tailLines;
}
/**
* Tries to delete a file. Emits a warning if the file was unable to be deleted.
*
* @param file File to delete.
* @return true if the file was deleted.
*/
public static boolean tryDelete(File file) {
boolean deleted = FileUtils.deleteQuietly(file);
if (deleted)
logger.debug("Deleted " + file);
else if (file.exists())
logger.warn("Unable to delete " + file);
return deleted;
}
/**
* Writes the an embedded resource to a temp file.
* File is not scheduled for deletion and must be cleaned up by the caller.
* @param resource Embedded resource.
* @return Path to the temp file with the contents of the resource.
*/
public static File writeTempResource(Resource resource) {
File temp;
try {
temp = File.createTempFile(FilenameUtils.getBaseName(resource.getPath()) + ".", "." + FilenameUtils.getExtension(resource.getPath()));
} catch (IOException e) {
throw new UserException.BadTmpDir(e.getMessage());
}
writeResource(resource, temp);
return temp;
}
/**
* Writes the an embedded resource to a file.
* File is not scheduled for deletion and must be cleaned up by the caller.
* @param resource Embedded resource.
* @param file File path to write.
*/
public static void writeResource(Resource resource, File file) {
String path = resource.getPath();
Class<?> clazz = resource.getRelativeClass();
InputStream inputStream = null;
OutputStream outputStream = null;
try {
if (clazz == null) {
inputStream = ClassLoader.getSystemResourceAsStream(path);
if (inputStream == null)
throw new IllegalArgumentException("Resource not found: " + path);
} else {
inputStream = clazz.getResourceAsStream(path);
if (inputStream == null)
throw new IllegalArgumentException("Resource not found relative to " + clazz + ": " + path);
}
outputStream = FileUtils.openOutputStream(file);
org.apache.commons.io.IOUtils.copy(inputStream, outputStream);
} catch (IOException e) {
throw new StingException(String.format("Unable to copy resource '%s' to '%s'", path, file), e);
} finally {
org.apache.commons.io.IOUtils.closeQuietly(inputStream);
org.apache.commons.io.IOUtils.closeQuietly(outputStream);
}
}
}

53
public/java/src/org/broadinstitute/sting/utils/io/Resource.java 100644
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@ -0,0 +1,53 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.io;
/**
* Stores a resource by path and a relative class.
*/
public class Resource {
private final String path;
private final Class<?> relativeClass;
/**
* Create a resource with a path and a relative class.
* @param path Relative or absolute path to the class.
* @param relativeClass Relative class to use as a class loader and for a relative package.
*
* If the relative class is null then the system classloader will be used and the path must be absolute.
*/
public Resource(String path, Class<?> relativeClass) {
this.path = path;
this.relativeClass = relativeClass;
}
public Class<?> getRelativeClass() {
return relativeClass;
}
public String getPath() {
return path;
}
}

88
public/java/src/org/broadinstitute/sting/utils/pileup/FragmentPileup.java
View File

@ -1,9 +1,10 @@
package org.broadinstitute.sting.utils.pileup;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import java.util.*;
/**
* An easy to access fragment-based pileup, which contains two separate pileups. The first
@ -13,31 +14,51 @@ import java.util.Map;
*
* Based on the original code by E. Banks
*
* TODO -- technically we could generalize this code to support a pseudo-duplicate marking
* TODO -- algorithm that could collect all duplicates into a single super pileup element
* Oct 21: note that the order of the oneReadPileup and twoReadPileups are not
* defined. The algorithms that produce these lists are in fact producing
* lists of Pileup elements *NOT* sorted by alignment start position of the underlying
* reads.
*
* User: depristo
* Date: 3/26/11
* Time: 10:09 PM
*/
public class FragmentPileup {
final Collection<PileupElement> oneReadPile;
final Collection<TwoReadPileupElement> twoReadPile = new ArrayList<TwoReadPileupElement>();
Collection<PileupElement> oneReadPile = null;
Collection<TwoReadPileupElement> twoReadPile = null;
protected enum FragmentMatchingAlgorithm {
ORIGINAL,
skipNonOverlapping,
}
/**
* Create a new Fragment-based pileup from the standard read-based pileup
* @param pileup
*/
public FragmentPileup(ReadBackedPileup pileup) {
Map<String, PileupElement> nameMap = new HashMap<String, PileupElement>();
skipNonOverlapping(pileup);
}
/** For performance testing only */
protected FragmentPileup(ReadBackedPileup pileup, FragmentMatchingAlgorithm algorithm) {
switch ( algorithm ) {
case ORIGINAL: oldSlowCalculation(pileup); break;
case skipNonOverlapping: skipNonOverlapping(pileup); break;
}
}
private final void oldSlowCalculation(final ReadBackedPileup pileup) {
final Map<String, PileupElement> nameMap = new HashMap<String, PileupElement>(pileup.size());
// build an initial map, grabbing all of the multi-read fragments
for ( PileupElement p : pileup ) {
String readName = p.getRead().getReadName();
for ( final PileupElement p : pileup ) {
final String readName = p.getRead().getReadName();
PileupElement pe1 = nameMap.get(readName);
final PileupElement pe1 = nameMap.get(readName);
if ( pe1 != null ) {
// assumes we have at most 2 reads per fragment
if ( twoReadPile == null ) twoReadPile = new ArrayList<TwoReadPileupElement>();
twoReadPile.add(new TwoReadPileupElement(pe1, p));
nameMap.remove(readName);
} else {
@ -45,17 +66,54 @@ public class FragmentPileup {
}
}
// now set the one Read pile to the values in the nameMap with only a single read
oneReadPile = nameMap.values();
}
private final void skipNonOverlapping(final ReadBackedPileup pileup) {
Map<String, PileupElement> nameMap = null;
// build an initial map, grabbing all of the multi-read fragments
for ( final PileupElement p : pileup ) {
final SAMRecord read = p.getRead();
final int mateStart = read.getMateAlignmentStart();
if ( mateStart == 0 || mateStart > read.getAlignmentEnd() ) {
// if we know that this read won't overlap its mate, or doesn't have one, jump out early
if ( oneReadPile == null ) oneReadPile = new ArrayList<PileupElement>(pileup.size()); // lazy init
oneReadPile.add(p);
} else {
// the read might overlap it's mate, or is the rightmost read of a pair
final String readName = p.getRead().getReadName();
final PileupElement pe1 = nameMap == null ? null : nameMap.get(readName);
if ( pe1 != null ) {
// assumes we have at most 2 reads per fragment
if ( twoReadPile == null ) twoReadPile = new ArrayList<TwoReadPileupElement>(); // lazy init
twoReadPile.add(new TwoReadPileupElement(pe1, p));
nameMap.remove(readName);
} else {
if ( nameMap == null ) nameMap = new HashMap<String, PileupElement>(pileup.size()); // lazy init
nameMap.put(readName, p);
}
}
}
// add all of the reads that are potentially overlapping but whose mate never showed
// up to the oneReadPile
if ( nameMap != null && ! nameMap.isEmpty() ) {
if ( oneReadPile == null )
oneReadPile = nameMap.values();
else
oneReadPile.addAll(nameMap.values());
}
}
/**
* Gets the pileup elements containing two reads, in no particular order
*
* @return
*/
public Collection<TwoReadPileupElement> getTwoReadPileup() {
return twoReadPile;
return twoReadPile == null ? Collections.<TwoReadPileupElement>emptyList() : twoReadPile;
}
/**
@ -64,7 +122,7 @@ public class FragmentPileup {
* @return
*/
public Collection<PileupElement> getOneReadPileup() {
return oneReadPile;
return oneReadPile == null ? Collections.<PileupElement>emptyList() : oneReadPile;
}
/**

23
public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
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@ -4,6 +4,7 @@ import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
/**
@ -12,7 +13,7 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
* Date: Apr 14, 2009
* Time: 8:54:05 AM
*/
public class PileupElement {
public class PileupElement implements Comparable<PileupElement> {
public static final byte DELETION_BASE = BaseUtils.D;
public static final byte DELETION_QUAL = (byte) 16;
public static final byte A_FOLLOWED_BY_INSERTION_BASE = (byte) 87;
@ -75,6 +76,20 @@ public class PileupElement {
return isDeletion() ? DELETION_QUAL : read.getBaseQualities()[offset];
}
@Override
public int compareTo(final PileupElement pileupElement) {
if ( offset < pileupElement.offset )
return -1;
else if ( offset > pileupElement.offset )
return 1;
else if ( read.getAlignmentStart() < pileupElement.read.getAlignmentStart() )
return -1;
else if ( read.getAlignmentStart() > pileupElement.read.getAlignmentStart() )
return 1;
else
return 0;
}
// --------------------------------------------------------------------------
//
// Reduced read accessors
@ -82,16 +97,16 @@ public class PileupElement {
// --------------------------------------------------------------------------
public boolean isReducedRead() {
return ReadUtils.isReducedRead(getRead());
return ((GATKSAMRecord)read).isReducedRead();
}
public int getReducedCount() {
if ( ! isReducedRead() ) throw new IllegalArgumentException("Cannot get reduced count for non-reduced read " + getRead().getReadName());
return ReadUtils.getReducedCount(getRead(), offset);
return ((GATKSAMRecord)read).getReducedCount(offset);
}
public byte getReducedQual() {
if ( ! isReducedRead() ) throw new IllegalArgumentException("Cannot get reduced qual for non-reduced read " + getRead().getReadName());
return ReadUtils.getReducedQual(getRead(), offset);
return getQual();
}
}

133
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@ -0,0 +1,133 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.runtime;
import org.apache.commons.io.IOUtils;
import org.apache.commons.io.output.NullOutputStream;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.io.HardThresholdingOutputStream;
import java.io.*;
import java.util.EnumMap;
/**
* Stream output captured from a stream.
*/
public class CapturedStreamOutput extends StreamOutput {
private final InputStream processStream;
private final EnumMap<StreamLocation, OutputStream> outputStreams = new EnumMap<StreamLocation, OutputStream>(StreamLocation.class);
/**
* The byte stream to capture content or null if no output string content was requested.
*/
private final ByteArrayOutputStream bufferStream;
/**
* True if the buffer is truncated.
*/
private boolean bufferTruncated = false;
/**
* @param settings Settings that define what to capture.
* @param processStream Stream to capture output.
* @param standardStream Stream to write debug output.
*/
public CapturedStreamOutput(OutputStreamSettings settings, InputStream processStream, PrintStream standardStream) {
this.processStream = processStream;
int bufferSize = settings.getBufferSize();
this.bufferStream = (bufferSize < 0) ? new ByteArrayOutputStream() : new ByteArrayOutputStream(bufferSize);
for (StreamLocation location : settings.getStreamLocations()) {
OutputStream outputStream;
switch (location) {
case Buffer:
if (bufferSize < 0) {
outputStream = this.bufferStream;
} else {
outputStream = new HardThresholdingOutputStream(bufferSize) {
@Override
protected OutputStream getStream() throws IOException {
return bufferTruncated ? NullOutputStream.NULL_OUTPUT_STREAM : bufferStream;
}
@Override
protected void thresholdReached() throws IOException {
bufferTruncated = true;
}
};
}
break;
case File:
try {
outputStream = new FileOutputStream(settings.getOutputFile(), settings.isAppendFile());
} catch (IOException e) {
throw new UserException.BadInput(e.getMessage());
}
break;
case Standard:
outputStream = standardStream;
break;
default:
throw new ReviewedStingException("Unexpected stream location: " + location);
}
this.outputStreams.put(location, outputStream);
}
}
@Override
public byte[] getBufferBytes() {
return bufferStream.toByteArray();
}
@Override
public boolean isBufferTruncated() {
return bufferTruncated;
}
/**
* Drain the input stream to keep the process from backing up until it's empty.
* File streams will be closed automatically when this method returns.
*
* @throws java.io.IOException When unable to read or write.
*/
public void readAndClose() throws IOException {
try {
byte[] buf = new byte[4096];
int readCount;
while ((readCount = processStream.read(buf)) >= 0)
for (OutputStream outputStream : this.outputStreams.values()) {
outputStream.write(buf, 0, readCount);
}
} finally {
for (StreamLocation location : this.outputStreams.keySet()) {
OutputStream outputStream = this.outputStreams.get(location);
outputStream.flush();
if (location != StreamLocation.Standard)
IOUtils.closeQuietly(outputStream);
}
}
}
}

115
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@ -0,0 +1,115 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.runtime;
import java.io.File;
import java.util.Collections;
import java.util.EnumSet;
import java.util.Set;
/**
* Settings that define text to write to the process stdin.
*/
public class InputStreamSettings {
private final EnumSet<StreamLocation> streamLocations = EnumSet.noneOf(StreamLocation.class);
private byte[] inputBuffer;
private File inputFile;
public InputStreamSettings() {
}
/**
* @param inputBuffer String to write to stdin.
*/
public InputStreamSettings(String inputBuffer) {
setInputBuffer(inputBuffer);
}
/**
* @param inputFile File to write to stdin.
*/
public InputStreamSettings(File inputFile) {
setInputFile(inputFile);
}
/**
* @param inputBuffer String to write to stdin.
* @param inputFile File to write to stdin.
*/
public InputStreamSettings(byte[] inputBuffer, File inputFile) {
setInputBuffer(inputBuffer);
setInputFile(inputFile);
}
public Set<StreamLocation> getStreamLocations() {
return Collections.unmodifiableSet(streamLocations);
}
public byte[] getInputBuffer() {
return inputBuffer;
}
public void setInputBuffer(String inputBuffer) {
if (inputBuffer == null)
throw new IllegalArgumentException("inputBuffer cannot be null");
this.streamLocations.add(StreamLocation.Buffer);
this.inputBuffer = inputBuffer.getBytes();
}
public void setInputBuffer(byte[] inputBuffer) {
if (inputBuffer == null)
throw new IllegalArgumentException("inputBuffer cannot be null");
this.streamLocations.add(StreamLocation.Buffer);
this.inputBuffer = inputBuffer;
}
public void clearInputBuffer() {
this.streamLocations.remove(StreamLocation.Buffer);
this.inputBuffer = null;
}
public File getInputFile() {
return inputFile;
}
public void setInputFile(File inputFile) {
if (inputFile == null)
throw new IllegalArgumentException("inputFile cannot be null");
this.streamLocations.add(StreamLocation.File);
this.inputFile = inputFile;
}
public void clearInputFile() {
this.streamLocations.remove(StreamLocation.File);
this.inputFile = null;
}
public void setInputStandard(boolean inputStandard) {
if (inputStandard)
this.streamLocations.add(StreamLocation.Standard);
else
this.streamLocations.remove(StreamLocation.Standard);
}
}

126
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@ -0,0 +1,126 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.runtime;
import java.io.File;
import java.util.Collections;
import java.util.EnumSet;
import java.util.Set;
/**
* Settings that define text to capture from a process stream.
*/
public class OutputStreamSettings {
private final EnumSet<StreamLocation> streamLocations = EnumSet.noneOf(StreamLocation.class);
private int bufferSize;
private File outputFile;
private boolean appendFile;
public OutputStreamSettings() {
}
/**
* @param bufferSize The number of bytes to capture, or -1 for unlimited.
*/
public OutputStreamSettings(int bufferSize) {
setBufferSize(bufferSize);
}
/**
* @param outputFile The file to write output to.
*/
public OutputStreamSettings(File outputFile) {
setOutputFile(outputFile);
}
/**
* @param outputFile The file to write output to.
* @param append true if the output file should be appended to.
*/
public OutputStreamSettings(File outputFile, boolean append) {
setOutputFile(outputFile, append);
}
public OutputStreamSettings(int bufferSize, File outputFile, boolean appendFile) {
setBufferSize(bufferSize);
setOutputFile(outputFile, appendFile);
}
public Set<StreamLocation> getStreamLocations() {
return Collections.unmodifiableSet(streamLocations);
}
public int getBufferSize() {
return bufferSize;
}
public void setBufferSize(int bufferSize) {
this.streamLocations.add(StreamLocation.Buffer);
this.bufferSize = bufferSize;
}
public void clearBufferSize() {
this.streamLocations.remove(StreamLocation.Buffer);
this.bufferSize = 0;
}
public File getOutputFile() {
return outputFile;
}
public boolean isAppendFile() {
return appendFile;
}
/**
* Overwrites the outputFile with the process output.
*
* @param outputFile File to overwrite.
*/
public void setOutputFile(File outputFile) {
setOutputFile(outputFile, false);
}
public void setOutputFile(File outputFile, boolean append) {
if (outputFile == null)
throw new IllegalArgumentException("outputFile cannot be null");
streamLocations.add(StreamLocation.File);
this.outputFile = outputFile;
this.appendFile = append;
}
public void clearOutputFile() {
streamLocations.remove(StreamLocation.File);
this.outputFile = null;
this.appendFile = false;
}
public void printStandard(boolean print) {
if (print)
this.streamLocations.add(StreamLocation.Standard);
else
this.streamLocations.remove(StreamLocation.Standard);
}
}

363
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@ -0,0 +1,363 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.runtime;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.*;
/**
* Facade to Runtime.exec() and java.lang.Process. Handles
* running a process to completion and returns stdout and stderr
* as strings. Creates separate threads for reading stdout and stderr,
* then reuses those threads for each process most efficient use is
* to create one of these and use it repeatedly. Instances are not
* thread-safe, however.
*
* TODO: java.io sometimes zombies the backround threads locking up on read().
* Supposedly NIO has better ways of interrupting a blocked stream but will
* require a little bit of refactoring.
*
* @author Michael Koehrsen
* @author Khalid Shakir
*/
public class ProcessController {
private static Logger logger = Logger.getLogger(ProcessController.class);
private static enum ProcessStream {Stdout, Stderr}
// Tracks running processes.
private static final Set<ProcessController> running = Collections.synchronizedSet(new HashSet<ProcessController>());
// Tracks this running process.
private Process process;
// Threads that capture stdout and stderr
private final OutputCapture stdoutCapture;
private final OutputCapture stderrCapture;
// When a caller destroyes a controller a new thread local version will be created
private boolean destroyed = false;
// Communication channels with output capture threads
// Holds the stdout and stderr sent to the background capture threads
private final Map<ProcessStream, CapturedStreamOutput> toCapture =
new EnumMap<ProcessStream, CapturedStreamOutput>(ProcessStream.class);
// Holds the results of the capture from the background capture threads.
// May be the content via toCapture or an StreamOutput.EMPTY if the capture was interrupted.
private final Map<ProcessStream, StreamOutput> fromCapture =
new EnumMap<ProcessStream, StreamOutput>(ProcessStream.class);
// Useful for debugging if background threads have shut down correctly
private static int nextControllerId = 0;
private final int controllerId;
public ProcessController() {
// Start the background threads for this controller.
synchronized (running) {
controllerId = nextControllerId++;
}
stdoutCapture = new OutputCapture(ProcessStream.Stdout, controllerId);
stderrCapture = new OutputCapture(ProcessStream.Stderr, controllerId);
stdoutCapture.start();
stderrCapture.start();
}
/**
* Returns a thread local ProcessController.
* Should NOT be closed when finished so it can be reused by the thread.
*
* @return a thread local ProcessController.
*/
public static ProcessController getThreadLocal() {
// If the local controller was destroyed get a fresh instance.
if (threadProcessController.get().destroyed)
threadProcessController.remove();
return threadProcessController.get();
}
/**
* Thread local process controller container.
*/
private static final ThreadLocal<ProcessController> threadProcessController =
new ThreadLocal<ProcessController>() {
@Override
protected ProcessController initialValue() {
return new ProcessController();
}
};
/**
* Similar to Runtime.exec() but drains the output and error streams.
*
* @param command Command to run.
* @return The result code.
*/
public static int exec(String[] command) {
ProcessController controller = ProcessController.getThreadLocal();
return controller.exec(new ProcessSettings(command)).getExitValue();
}
/**
* Executes a command line program with the settings and waits for it to return,
* processing the output on a background thread.
*
* @param settings Settings to be run.
* @return The output of the command.
*/
public ProcessOutput exec(ProcessSettings settings) {
if (destroyed)
throw new IllegalStateException("This controller was destroyed");
ProcessBuilder builder = new ProcessBuilder(settings.getCommand());
builder.directory(settings.getDirectory());
Map<String, String> settingsEnvironment = settings.getEnvironment();
if (settingsEnvironment != null) {
Map<String, String> builderEnvironment = builder.environment();
builderEnvironment.clear();
builderEnvironment.putAll(settingsEnvironment);
}
builder.redirectErrorStream(settings.isRedirectErrorStream());
StreamOutput stdout = null;
StreamOutput stderr = null;
// Start the process running.
try {
synchronized (toCapture) {
process = builder.start();
}
running.add(this);
} catch (IOException e) {
throw new ReviewedStingException("Unable to start command: " + StringUtils.join(builder.command(), " "));
}
int exitCode;
try {
// Notify the background threads to start capturing.
synchronized (toCapture) {
toCapture.put(ProcessStream.Stdout,
new CapturedStreamOutput(settings.getStdoutSettings(), process.getInputStream(), System.out));
toCapture.put(ProcessStream.Stderr,
new CapturedStreamOutput(settings.getStderrSettings(), process.getErrorStream(), System.err));
toCapture.notifyAll();
}
// Write stdin content
InputStreamSettings stdinSettings = settings.getStdinSettings();
Set<StreamLocation> streamLocations = stdinSettings.getStreamLocations();
if (!streamLocations.isEmpty()) {
try {
OutputStream stdinStream = process.getOutputStream();
for (StreamLocation location : streamLocations) {
InputStream inputStream;
switch (location) {
case Buffer:
inputStream = new ByteArrayInputStream(stdinSettings.getInputBuffer());
break;
case File:
try {
inputStream = FileUtils.openInputStream(stdinSettings.getInputFile());
} catch (IOException e) {
throw new UserException.BadInput(e.getMessage());
}
break;
case Standard:
inputStream = System.in;
break;
default:
throw new ReviewedStingException("Unexpected stream location: " + location);
}
try {
IOUtils.copy(inputStream, stdinStream);
} finally {
if (location != StreamLocation.Standard)
IOUtils.closeQuietly(inputStream);
}
}
stdinStream.flush();
} catch (IOException e) {
throw new ReviewedStingException("Error writing to stdin on command: " + StringUtils.join(builder.command(), " "), e);
}
}
// Wait for the process to complete.
try {
process.getOutputStream().close();
process.waitFor();
} catch (IOException e) {
throw new ReviewedStingException("Unable to close stdin on command: " + StringUtils.join(builder.command(), " "), e);
} catch (InterruptedException e) {
throw new ReviewedStingException("Process interrupted", e);
} finally {
while (!destroyed && stdout == null || stderr == null) {
synchronized (fromCapture) {
if (fromCapture.containsKey(ProcessStream.Stdout))
stdout = fromCapture.remove(ProcessStream.Stdout);
if (fromCapture.containsKey(ProcessStream.Stderr))
stderr = fromCapture.remove(ProcessStream.Stderr);
try {
if (stdout == null || stderr == null)
fromCapture.wait();
} catch (InterruptedException e) {
// Log the error, ignore the interrupt and wait patiently
// for the OutputCaptures to (via finally) return their
// stdout and stderr.
logger.error(e);
}
}
}
if (destroyed) {
if (stdout == null)
stdout = StreamOutput.EMPTY;
if (stderr == null)
stderr = StreamOutput.EMPTY;
}
}
} finally {
synchronized (toCapture) {
exitCode = process.exitValue();
process = null;
}
running.remove(this);
}
return new ProcessOutput(exitCode, stdout, stderr);
}
/**
* @return The set of still running processes.
*/
public static Set<ProcessController> getRunning() {
synchronized (running) {
return new HashSet<ProcessController>(running);
}
}
/**
* Stops the process from running and tries to ensure process is cleaned up properly.
* NOTE: sub-processes started by process may be zombied with their parents set to pid 1.
* NOTE: capture threads may block on read.
* TODO: Try to use NIO to interrupt streams.
*/
public void tryDestroy() {
destroyed = true;
synchronized (toCapture) {
if (process != null) {
process.destroy();
IOUtils.closeQuietly(process.getInputStream());
IOUtils.closeQuietly(process.getErrorStream());
}
stdoutCapture.interrupt();
stderrCapture.interrupt();
toCapture.notifyAll();
}
}
@Override
protected void finalize() throws Throwable {
try {
tryDestroy();
} catch (Exception e) {
logger.error(e);
}
super.finalize();
}
private class OutputCapture extends Thread {
private final int controllerId;
private final ProcessStream key;
/**
* Reads in the output of a stream on a background thread to keep the output pipe from backing up and freezing the called process.
*
* @param key The stdout or stderr key for this output capture.
* @param controllerId Unique id of the controller.
*/
public OutputCapture(ProcessStream key, int controllerId) {
super(String.format("OutputCapture-%d-%s-%s-%d", controllerId, key.name().toLowerCase(),
Thread.currentThread().getName(), Thread.currentThread().getId()));
this.controllerId = controllerId;
this.key = key;
setDaemon(true);
}
/**
* Runs the capture.
*/
@Override
public void run() {
while (!destroyed) {
StreamOutput processStream = StreamOutput.EMPTY;
try {
// Wait for a new input stream to be passed from this process controller.
CapturedStreamOutput capturedProcessStream = null;
while (!destroyed && capturedProcessStream == null) {
synchronized (toCapture) {
if (toCapture.containsKey(key)) {
capturedProcessStream = toCapture.remove(key);
} else {
toCapture.wait();
}
}
}
if (!destroyed) {
// Read in the input stream
processStream = capturedProcessStream;
capturedProcessStream.readAndClose();
}
} catch (InterruptedException e) {
logger.info("OutputCapture interrupted, exiting");
break;
} catch (IOException e) {
logger.error("Error reading process output", e);
} finally {
// Send the string back to the process controller.
synchronized (fromCapture) {
fromCapture.put(key, processStream);
fromCapture.notify();
}
}
}
}
}
}

56
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@ -0,0 +1,56 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.runtime;
public class ProcessOutput {
private final int exitValue;
private final StreamOutput stdout;
private final StreamOutput stderr;
/**
* The output of a process.
*
* @param exitValue The exit value.
* @param stdout The capture of stdout as defined by the stdout OutputStreamSettings.
* @param stderr The capture of stderr as defined by the stderr OutputStreamSettings.
*/
public ProcessOutput(int exitValue, StreamOutput stdout, StreamOutput stderr) {
this.exitValue = exitValue;
this.stdout = stdout;
this.stderr = stderr;
}
public int getExitValue() {
return exitValue;
}
public StreamOutput getStdout() {
return stdout;
}
public StreamOutput getStderr() {
return stderr;
}
}

140
public/java/src/org/broadinstitute/sting/utils/runtime/ProcessSettings.java 100755
View File

@ -0,0 +1,140 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.runtime;
import com.sun.corba.se.spi.orbutil.fsm.Input;
import java.io.File;
import java.util.Map;
public class ProcessSettings {
private String[] command;
private Map<String, String> environment;
private File directory;
private boolean redirectErrorStream;
private InputStreamSettings stdinSettings;
private OutputStreamSettings stdoutSettings;
private OutputStreamSettings stderrSettings;
/**
* @param command Command line to run.
*/
public ProcessSettings(String[] command) {
this(command, false, null, null, null, null, null);
}
/**
* @param command Command line to run.
* @param redirectErrorStream true if stderr should be sent to stdout.
* @param environment Environment settings to override System.getEnv, or null to use System.getEnv.
* @param directory The directory to run the command in, or null to run in the current directory.
* @param stdinSettings Settings for writing to the process stdin.
* @param stdoutSettings Settings for capturing the process stdout.
* @param stderrSettings Setting for capturing the process stderr.
*/
public ProcessSettings(String[] command, boolean redirectErrorStream, File directory, Map<String, String> environment,
InputStreamSettings stdinSettings, OutputStreamSettings stdoutSettings, OutputStreamSettings stderrSettings) {
this.command = checkCommand(command);
this.redirectErrorStream = redirectErrorStream;
this.directory = directory;
this.environment = environment;
this.stdinSettings = checkSettings(stdinSettings);
this.stdoutSettings = checkSettings(stdoutSettings);
this.stderrSettings = checkSettings(stderrSettings);
}
public String[] getCommand() {
return command;
}
public void setCommand(String[] command) {
this.command = checkCommand(command);
}
public boolean isRedirectErrorStream() {
return redirectErrorStream;
}
public void setRedirectErrorStream(boolean redirectErrorStream) {
this.redirectErrorStream = redirectErrorStream;
}
public File getDirectory() {
return directory;
}
public void setDirectory(File directory) {
this.directory = directory;
}
public Map<String, String> getEnvironment() {
return environment;
}
public void setEnvironment(Map<String, String> environment) {
this.environment = environment;
}
public InputStreamSettings getStdinSettings() {
return stdinSettings;
}
public void setStdinSettings(InputStreamSettings stdinSettings) {
this.stdinSettings = checkSettings(stdinSettings);
}
public OutputStreamSettings getStdoutSettings() {
return stdoutSettings;
}
public void setStdoutSettings(OutputStreamSettings stdoutSettings) {
this.stdoutSettings = checkSettings(stdoutSettings);
}
public OutputStreamSettings getStderrSettings() {
return stderrSettings;
}
public void setStderrSettings(OutputStreamSettings stderrSettings) {
this.stderrSettings = checkSettings(stderrSettings);
}
protected String[] checkCommand(String[] command) {
if (command == null)
throw new IllegalArgumentException("Command is not allowed to be null");
for (String s: command)
if (s == null)
throw new IllegalArgumentException("Command is not allowed to contain nulls");
return command;
}
protected InputStreamSettings checkSettings(InputStreamSettings settings) {
return settings == null ? new InputStreamSettings() : settings;
}
protected OutputStreamSettings checkSettings(OutputStreamSettings settings) {
return settings == null ? new OutputStreamSettings() : settings;
}
}

32
public/java/src/org/broadinstitute/sting/utils/runtime/StreamLocation.java 100755
View File

@ -0,0 +1,32 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.runtime;
/**
* Where to read/write a stream
*/
public enum StreamLocation {
Buffer, File, Standard
}

68
public/java/src/org/broadinstitute/sting/utils/runtime/StreamOutput.java 100755
View File

@ -0,0 +1,68 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.runtime;
/**
* The content of stdout or stderr.
*/
public abstract class StreamOutput {
/**
* Empty stream output when no output is captured due to an error.
*/
public static final StreamOutput EMPTY = new StreamOutput() {
@Override
public byte[] getBufferBytes() {
return new byte[0];
}
@Override
public boolean isBufferTruncated() {
return false;
}
};
/**
* Returns the content as a string.
*
* @return The content as a string.
*/
public String getBufferString() {
return new String(getBufferBytes());
}
/**
* Returns the content as a string.
*
* @return The content as a string.
*/
public abstract byte[] getBufferBytes();
/**
* Returns true if the buffer was truncated.
*
* @return true if the buffer was truncated.
*/
public abstract boolean isBufferTruncated();
}

102
public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
View File

@ -2,11 +2,15 @@ package org.broadinstitute.sting.utils.sam;
import net.sf.samtools.*;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import java.util.*;
/**
* @author aaron
@ -29,7 +33,7 @@ public class ArtificialSAMUtils {
File outFile = new File(filename);
SAMFileWriter out = new SAMFileWriterFactory().makeBAMWriter(header, true, outFile);
for (int x = startingChromosome; x < startingChromosome + numberOfChromosomes; x++) {
for (int readNumber = 1; readNumber < readsPerChomosome; readNumber++) {
out.addAlignment(createArtificialRead(header, "Read_" + readNumber, x - startingChromosome, readNumber, DEFAULT_READ_LENGTH));
@ -134,6 +138,7 @@ public class ArtificialSAMUtils {
/**
* Create an artificial read based on the parameters. The cigar string will be *M, where * is the length of the read
*
*
* @param header the SAM header to associate the read with
* @param name the name of the read
* @param refIndex the reference index, i.e. what chromosome to associate it with
@ -142,11 +147,11 @@ public class ArtificialSAMUtils {
*
* @return the artificial read
*/
public static SAMRecord createArtificialRead( SAMFileHeader header, String name, int refIndex, int alignmentStart, int length ) {
public static GATKSAMRecord createArtificialRead(SAMFileHeader header, String name, int refIndex, int alignmentStart, int length) {
if( (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart != SAMRecord.NO_ALIGNMENT_START) ||
(refIndex != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart == SAMRecord.NO_ALIGNMENT_START) )
(refIndex != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart == SAMRecord.NO_ALIGNMENT_START) )
throw new ReviewedStingException("Invalid alignment start for artificial read, start = " + alignmentStart);
SAMRecord record = new SAMRecord(header);
GATKSAMRecord record = new GATKSAMRecord(header);
record.setReadName(name);
record.setReferenceIndex(refIndex);
record.setAlignmentStart(alignmentStart);
@ -166,6 +171,7 @@ public class ArtificialSAMUtils {
if (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
record.setReadUnmappedFlag(true);
}
return record;
}
@ -181,19 +187,51 @@ public class ArtificialSAMUtils {
*
* @return the artificial read
*/
public static SAMRecord createArtificialRead( SAMFileHeader header, String name, int refIndex, int alignmentStart, byte[] bases, byte[] qual ) {
public static GATKSAMRecord createArtificialRead( SAMFileHeader header, String name, int refIndex, int alignmentStart, byte[] bases, byte[] qual ) {
if (bases.length != qual.length) {
throw new ReviewedStingException("Passed in read string is different length then the quality array");
}
SAMRecord rec = createArtificialRead(header, name, refIndex, alignmentStart, bases.length);
GATKSAMRecord rec = createArtificialRead(header, name, refIndex, alignmentStart, bases.length);
rec.setReadBases(bases);
rec.setBaseQualities(qual);
if (refIndex == -1) {
rec.setReadUnmappedFlag(true);
}
return rec;
}
public final static List<SAMRecord> createPair(SAMFileHeader header, String name, int readLen, int leftStart, int rightStart, boolean leftIsFirst, boolean leftIsNegative) {
SAMRecord left = ArtificialSAMUtils.createArtificialRead(header, name, 0, leftStart, readLen);
SAMRecord right = ArtificialSAMUtils.createArtificialRead(header, name, 0, rightStart, readLen);
left.setReadPairedFlag(true);
right.setReadPairedFlag(true);
left.setProperPairFlag(true);
right.setProperPairFlag(true);
left.setFirstOfPairFlag(leftIsFirst);
right.setFirstOfPairFlag(! leftIsFirst);
left.setReadNegativeStrandFlag(leftIsNegative);
left.setMateNegativeStrandFlag(!leftIsNegative);
right.setReadNegativeStrandFlag(!leftIsNegative);
right.setMateNegativeStrandFlag(leftIsNegative);
left.setMateAlignmentStart(right.getAlignmentStart());
right.setMateAlignmentStart(left.getAlignmentStart());
left.setMateReferenceIndex(0);
right.setMateReferenceIndex(0);
int isize = rightStart + readLen - leftStart;
left.setInferredInsertSize(isize);
right.setInferredInsertSize(-isize);
return Arrays.asList(left, right);
}
/**
* create an iterator containing the specified read piles
*
@ -255,4 +293,52 @@ public class ArtificialSAMUtils {
return new ArtificialSAMQueryIterator(startingChr, endingChr, readCount, unmappedReadCount, header);
}
private final static int ranIntInclusive(Random ran, int start, int stop) {
final int range = stop - start;
return ran.nextInt(range) + start;
}
/**
* Creates a read backed pileup containing up to pileupSize reads at refID 0 from header at loc with
* reads created that have readLen bases. Pairs are sampled from a gaussian distribution with mean insert
* size of insertSize and variation of insertSize / 10. The first read will be in the pileup, and the second
* may be, depending on where this sampled insertSize puts it.
* @param header
* @param loc
* @param readLen
* @param insertSize
* @param pileupSize
* @return
*/
public static ReadBackedPileup createReadBackedPileup(final SAMFileHeader header, final GenomeLoc loc, final int readLen, final int insertSize, final int pileupSize) {
final Random ran = new Random();
final boolean leftIsFirst = true;
final boolean leftIsNegative = false;
final int insertSizeVariation = insertSize / 10;
final int pos = loc.getStart();
final List<PileupElement> pileupElements = new ArrayList<PileupElement>();
for ( int i = 0; i < pileupSize / 2; i++ ) {
final String readName = "read" + i;
final int leftStart = ranIntInclusive(ran, 1, pos);
final int fragmentSize = (int)(ran.nextGaussian() * insertSizeVariation + insertSize);
final int rightStart = leftStart + fragmentSize - readLen;
if ( rightStart <= 0 ) continue;
List<SAMRecord> pair = createPair(header, readName, readLen, leftStart, rightStart, leftIsFirst, leftIsNegative);
final SAMRecord left = pair.get(0);
final SAMRecord right = pair.get(1);
pileupElements.add(new PileupElement(left, pos - leftStart));
if ( pos >= right.getAlignmentStart() && pos <= right.getAlignmentEnd() ) {
pileupElements.add(new PileupElement(right, pos - rightStart));
}
}
Collections.sort(pileupElements);
return new ReadBackedPileupImpl(loc, pileupElements);
}
}

23
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java
View File

@ -1,6 +1,7 @@
package org.broadinstitute.sting.utils.sam;
import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.utils.NGSPlatform;
/**
* @author ebanks
@ -15,16 +16,28 @@ public class GATKSAMReadGroupRecord extends SAMReadGroupRecord {
// the SAMReadGroupRecord data we're caching
private String mSample = null;
private String mPlatform = null;
private NGSPlatform mNGSPlatform = null;
// because some values can be null, we don't want to duplicate effort
private boolean retrievedSample = false;
private boolean retrievedPlatform = false;
private boolean retrievedNGSPlatform = false;
public GATKSAMReadGroupRecord(final String id) {
super(id);
}
public GATKSAMReadGroupRecord(SAMReadGroupRecord record) {
super(record.getReadGroupId(), record);
}
public GATKSAMReadGroupRecord(SAMReadGroupRecord record, NGSPlatform pl) {
super(record.getReadGroupId(), record);
setPlatform(pl.getDefaultPlatform());
mNGSPlatform = pl;
retrievedPlatform = retrievedNGSPlatform = true;
}
///////////////////////////////////////////////////////////////////////////////
// *** The following methods are overloaded to cache the appropriate data ***//
///////////////////////////////////////////////////////////////////////////////
@ -55,5 +68,15 @@ public class GATKSAMReadGroupRecord extends SAMReadGroupRecord {
super.setPlatform(s);
mPlatform = s;
retrievedPlatform = true;
retrievedNGSPlatform = false; // recalculate the NGSPlatform
}
public NGSPlatform getNGSPlatform() {
if ( ! retrievedNGSPlatform ) {
mNGSPlatform = NGSPlatform.fromReadGroupPL(getPlatform());
retrievedNGSPlatform = true;
}
return mNGSPlatform;
}
}

453
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
View File

@ -1,49 +1,56 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.sam;
import net.sf.samtools.*;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.NGSPlatform;
import java.lang.reflect.Method;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* @author ebanks
* @author ebanks, depristo
* GATKSAMRecord
*
* this class extends the samtools SAMRecord class and caches important
* this class extends the samtools BAMRecord class (and SAMRecord) and caches important
* (and oft-accessed) data that's not already cached by the SAMRecord class
*
* IMPORTANT NOTE: Because ReadGroups are not set through the SAMRecord,
* if they are ever modified externally then one must also invoke the
* setReadGroup() method here to ensure that the cache is kept up-to-date.
*
* 13 Oct 2010 - mhanna - this class is fundamentally flawed: it uses a decorator
* pattern to wrap a heavyweight object, which can lead
* to heinous side effects if the wrapping is not carefully
* done. Hopefully SAMRecord will become an interface and
* this will eventually be fixed.
*/
public class GATKSAMRecord extends SAMRecord {
// the underlying SAMRecord which we are wrapping
private final SAMRecord mRecord;
public class GATKSAMRecord extends BAMRecord {
// the SAMRecord data we're caching
private String mReadString = null;
private SAMReadGroupRecord mReadGroup = null;
private boolean mNegativeStrandFlag;
private boolean mUnmappedFlag;
private Boolean mSecondOfPairFlag = null;
private GATKSAMReadGroupRecord mReadGroup = null;
private byte[] reducedReadCounts = null;
// because some values can be null, we don't want to duplicate effort
private boolean retrievedReadGroup = false;
/** A private cache for the reduced read quality. Null indicates the value hasn't be fetched yet or isn't available */
private boolean lookedUpReducedReadQuality = false;
private Integer reducedReadQuality;
private boolean retrievedReduceReadCounts = false;
// These temporary attributes were added here to make life easier for
// certain algorithms by providing a way to label or attach arbitrary data to
@ -51,101 +58,112 @@ public class GATKSAMRecord extends SAMRecord {
// These attributes exist in memory only, and are never written to disk.
private Map<Object, Object> temporaryAttributes;
public GATKSAMRecord(SAMRecord record, boolean useOriginalBaseQualities, byte defaultBaseQualities) {
super(null); // it doesn't matter - this isn't used
if ( record == null )
throw new IllegalArgumentException("The SAMRecord argument cannot be null");
mRecord = record;
/**
* HACK TO CREATE GATKSAMRECORD WITH ONLY A HEADER FOR TESTING PURPOSES ONLY
* @param header
*/
public GATKSAMRecord(final SAMFileHeader header) {
this(new SAMRecord(header));
}
mNegativeStrandFlag = mRecord.getReadNegativeStrandFlag();
mUnmappedFlag = mRecord.getReadUnmappedFlag();
/**
* HACK TO CREATE GATKSAMRECORD BASED ONLY A SAMRECORD FOR TESTING PURPOSES ONLY
* @param read
*/
public GATKSAMRecord(final SAMRecord read) {
super(read.getHeader(), read.getMateReferenceIndex(),
read.getAlignmentStart(),
read.getReadName() != null ? (short)read.getReadNameLength() : 0,
(short)read.getMappingQuality(),
0,
read.getCigarLength(),
read.getFlags(),
read.getReadLength(),
read.getMateReferenceIndex(),
read.getMateAlignmentStart(),
read.getInferredInsertSize(),
new byte[]{});
super.clearAttributes();
}
// because attribute methods are declared to be final (and we can't overload them),
// we need to actually set all of the attributes here
List<SAMTagAndValue> attributes = record.getAttributes();
for ( SAMTagAndValue attribute : attributes )
setAttribute(attribute.tag, attribute.value);
// if we are using default quals, check if we need them, and add if necessary.
// 1. we need if reads are lacking or have incomplete quality scores
// 2. we add if defaultBaseQualities has a positive value
if (defaultBaseQualities >= 0) {
byte reads [] = record.getReadBases();
byte quals [] = record.getBaseQualities();
if (quals == null || quals.length < reads.length) {
byte new_quals [] = new byte [reads.length];
for (int i=0; i<reads.length; i++)
new_quals[i] = defaultBaseQualities;
record.setBaseQualities(new_quals);
}
}
// if we are using original quals, set them now if they are present in the record
if ( useOriginalBaseQualities ) {
byte[] originalQuals = mRecord.getOriginalBaseQualities();
if ( originalQuals != null )
mRecord.setBaseQualities(originalQuals);
}
public GATKSAMRecord(final SAMFileHeader header,
final int referenceSequenceIndex,
final int alignmentStart,
final short readNameLength,
final short mappingQuality,
final int indexingBin,
final int cigarLen,
final int flags,
final int readLen,
final int mateReferenceSequenceIndex,
final int mateAlignmentStart,
final int insertSize,
final byte[] variableLengthBlock) {
super(header, referenceSequenceIndex, alignmentStart, readNameLength, mappingQuality, indexingBin, cigarLen,
flags, readLen, mateReferenceSequenceIndex, mateAlignmentStart, insertSize, variableLengthBlock);
}
///////////////////////////////////////////////////////////////////////////////
// *** The following methods are overloaded to cache the appropriate data ***//
///////////////////////////////////////////////////////////////////////////////
@Override
public String getReadString() {
if ( mReadString == null )
mReadString = mRecord.getReadString();
mReadString = super.getReadString();
return mReadString;
}
@Override
public void setReadString(String s) {
mRecord.setReadString(s);
super.setReadString(s);
mReadString = s;
}
public SAMReadGroupRecord getReadGroup() {
@Override
public GATKSAMReadGroupRecord getReadGroup() {
if ( !retrievedReadGroup ) {
SAMReadGroupRecord tempReadGroup = mRecord.getReadGroup();
mReadGroup = (tempReadGroup == null ? tempReadGroup : new GATKSAMReadGroupRecord(tempReadGroup));
SAMReadGroupRecord tempReadGroup = super.getReadGroup();
mReadGroup = (tempReadGroup == null ? null : new GATKSAMReadGroupRecord(tempReadGroup));
retrievedReadGroup = true;
}
return mReadGroup;
}
public void setReadGroup(SAMReadGroupRecord record) {
mReadGroup = record;
/**
* Efficient caching accessor that returns the GATK NGSPlatform of this read
* @return
*/
public NGSPlatform getNGSPlatform() {
return getReadGroup().getNGSPlatform();
}
public boolean getReadUnmappedFlag() {
return mUnmappedFlag;
public void setReadGroup( final GATKSAMReadGroupRecord readGroup ) {
mReadGroup = readGroup;
retrievedReadGroup = true;
}
public void setReadUnmappedFlag(boolean b) {
mRecord.setReadUnmappedFlag(b);
mUnmappedFlag = b;
}
//
//
// Reduced read functions
//
//
public boolean getReadNegativeStrandFlag() {
return mNegativeStrandFlag;
}
public void setReadNegativeStrandFlag(boolean b) {
mRecord.setReadNegativeStrandFlag(b);
mNegativeStrandFlag = b;
}
public boolean getSecondOfPairFlag() {
if( mSecondOfPairFlag == null ) {
//not done in constructor because this method can't be called for
//all SAMRecords.
mSecondOfPairFlag = mRecord.getSecondOfPairFlag();
public byte[] getReducedReadCounts() {
if ( ! retrievedReduceReadCounts ) {
reducedReadCounts = getByteArrayAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
retrievedReduceReadCounts = true;
}
return mSecondOfPairFlag;
return reducedReadCounts;
}
public void setSecondOfPairFlag(boolean b) {
mRecord.setSecondOfPairFlag(b);
mSecondOfPairFlag = b;
public boolean isReducedRead() {
return getReducedReadCounts() != null;
}
public final byte getReducedCount(final int i) {
return getReducedReadCounts()[i];
}
/**
@ -201,269 +219,18 @@ public class GATKSAMRecord extends SAMRecord {
return null;
}
/**
* Removes the attribute that has the given key.
*
* Temporary attributes provide a way to label or attach arbitrary data to
* individual GATKSAMRecords. These attributes exist in memory only,
* and are never written to disk.
*
* @param key key
* @return The value that was associated with this key, or null.
*/
public Object removeTemporaryAttribute(Object key) {
if(temporaryAttributes != null) {
return temporaryAttributes.remove(key);
}
return null;
@Override
public int hashCode() {
return super.hashCode();
}
/////////////////////////////////////////////////////////////////////////////////
// *** The following methods just call the appropriate method in the record ***//
/////////////////////////////////////////////////////////////////////////////////
public String getReadName() { return mRecord.getReadName(); }
public int getReadNameLength() { return mRecord.getReadNameLength(); }
public void setReadName(String s) { mRecord.setReadName(s); }
public byte[] getReadBases() { return mRecord.getReadBases(); }
public void setReadBases(byte[] bytes) { mRecord.setReadBases(bytes); }
public int getReadLength() { return mRecord.getReadLength(); }
public byte[] getBaseQualities() { return mRecord.getBaseQualities(); }
public void setBaseQualities(byte[] bytes) { mRecord.setBaseQualities(bytes); }
public String getBaseQualityString() { return mRecord.getBaseQualityString(); }
public void setBaseQualityString(String s) { mRecord.setBaseQualityString(s); }
public byte[] getOriginalBaseQualities() { return mRecord.getOriginalBaseQualities(); }
public void setOriginalBaseQualities(byte[] bytes) { mRecord.setOriginalBaseQualities(bytes); }
public String getReferenceName() { return mRecord.getReferenceName(); }
public void setReferenceName(String s) { mRecord.setReferenceName(s); }
public Integer getReferenceIndex() { return mRecord.getReferenceIndex(); }
public void setReferenceIndex(int i) { mRecord.setReferenceIndex(i); }
public String getMateReferenceName() { return mRecord.getMateReferenceName(); }
public void setMateReferenceName(String s) { mRecord.setMateReferenceName(s); }
public Integer getMateReferenceIndex() { return mRecord.getMateReferenceIndex(); }
public void setMateReferenceIndex(int i) { mRecord.setMateReferenceIndex(i); }
public int getAlignmentStart() { return mRecord.getAlignmentStart(); }
public void setAlignmentStart(int i) { mRecord.setAlignmentStart(i); }
public int getAlignmentEnd() { return mRecord.getAlignmentEnd(); }
public int getUnclippedStart() { return mRecord.getUnclippedStart(); }
public int getUnclippedEnd() { return mRecord.getUnclippedEnd(); }
public void setAlignmentEnd(int i) { mRecord.setAlignmentEnd(i); }
public int getMateAlignmentStart() { return mRecord.getMateAlignmentStart(); }
public void setMateAlignmentStart(int i) { mRecord.setMateAlignmentStart(i); }
public int getInferredInsertSize() { return mRecord.getInferredInsertSize(); }
public void setInferredInsertSize(int i) { mRecord.setInferredInsertSize(i); }
public int getMappingQuality() { return mRecord.getMappingQuality(); }
public void setMappingQuality(int i) { mRecord.setMappingQuality(i); }
public String getCigarString() { return mRecord.getCigarString(); }
public void setCigarString(String s) { mRecord.setCigarString(s); }
public Cigar getCigar() { return mRecord.getCigar(); }
public int getCigarLength() { return mRecord.getCigarLength(); }
public void setCigar(Cigar cigar) { mRecord.setCigar(cigar); }
public int getFlags() { return mRecord.getFlags(); }
public void setFlags(int i) { mRecord.setFlags(i); }
public boolean getReadPairedFlag() { return mRecord.getReadPairedFlag(); }
public boolean getProperPairFlag() { return mRecord.getProperPairFlag(); }
public boolean getMateUnmappedFlag() { return mRecord.getMateUnmappedFlag(); }
public boolean getMateNegativeStrandFlag() { return mRecord.getMateNegativeStrandFlag(); }
public boolean getFirstOfPairFlag() { return mRecord.getFirstOfPairFlag(); }
public boolean getNotPrimaryAlignmentFlag() { return mRecord.getNotPrimaryAlignmentFlag(); }
public boolean getReadFailsVendorQualityCheckFlag() { return mRecord.getReadFailsVendorQualityCheckFlag(); }
public boolean getDuplicateReadFlag() { return mRecord.getDuplicateReadFlag(); }
public void setReadPairedFlag(boolean b) { mRecord.setReadPairedFlag(b); }
public void setProperPairFlag(boolean b) { mRecord.setProperPairFlag(b); }
public void setMateUnmappedFlag(boolean b) { mRecord.setMateUnmappedFlag(b); }
public void setMateNegativeStrandFlag(boolean b) { mRecord.setMateNegativeStrandFlag(b); }
public void setFirstOfPairFlag(boolean b) { mRecord.setFirstOfPairFlag(b); }
public void setNotPrimaryAlignmentFlag(boolean b) { mRecord.setNotPrimaryAlignmentFlag(b); }
public void setReadFailsVendorQualityCheckFlag(boolean b) { mRecord.setReadFailsVendorQualityCheckFlag(b); }
public void setDuplicateReadFlag(boolean b) { mRecord.setDuplicateReadFlag(b); }
public net.sf.samtools.SAMFileReader.ValidationStringency getValidationStringency() { return mRecord.getValidationStringency(); }
public void setValidationStringency(net.sf.samtools.SAMFileReader.ValidationStringency validationStringency) { mRecord.setValidationStringency(validationStringency); }
public Object getAttribute(final String tag) { return mRecord.getAttribute(tag); }
public Integer getIntegerAttribute(final String tag) {
if ( tag == ReadUtils.REDUCED_READ_QUALITY_TAG ) {
if ( ! lookedUpReducedReadQuality ) {
lookedUpReducedReadQuality = true;
reducedReadQuality = mRecord.getIntegerAttribute(tag);
}
return reducedReadQuality;
} else {
return mRecord.getIntegerAttribute(tag);
}
}
public Short getShortAttribute(final String tag) { return mRecord.getShortAttribute(tag); }
public Byte getByteAttribute(final String tag) { return mRecord.getByteAttribute(tag); }
public String getStringAttribute(final String tag) { return mRecord.getStringAttribute(tag); }
public Character getCharacterAttribute(final String tag) { return mRecord.getCharacterAttribute(tag); }
public Float getFloatAttribute(final String tag) { return mRecord.getFloatAttribute(tag); }
public byte[] getByteArrayAttribute(final String tag) { return mRecord.getByteArrayAttribute(tag); }
protected Object getAttribute(final short tag) {
Object attribute;
try {
Method method = mRecord.getClass().getDeclaredMethod("getAttribute",Short.TYPE);
method.setAccessible(true);
attribute = method.invoke(mRecord,tag);
}
catch(Exception ex) {
throw new ReviewedStingException("Unable to invoke getAttribute method",ex);
}
return attribute;
}
public void setAttribute(final String tag, final Object value) { mRecord.setAttribute(tag,value); }
protected void setAttribute(final short tag, final Object value) {
try {
Method method = mRecord.getClass().getDeclaredMethod("setAttribute",Short.TYPE,Object.class);
method.setAccessible(true);
method.invoke(mRecord,tag,value);
}
catch(Exception ex) {
throw new ReviewedStingException("Unable to invoke setAttribute method",ex);
}
}
public void clearAttributes() { mRecord.clearAttributes(); }
protected void setAttributes(final SAMBinaryTagAndValue attributes) {
try {
Method method = mRecord.getClass().getDeclaredMethod("setAttributes",SAMBinaryTagAndValue.class);
method.setAccessible(true);
method.invoke(mRecord,attributes);
}
catch(Exception ex) {
throw new ReviewedStingException("Unable to invoke setAttributes method",ex);
}
}
protected SAMBinaryTagAndValue getBinaryAttributes() {
SAMBinaryTagAndValue binaryAttributes;
try {
Method method = mRecord.getClass().getDeclaredMethod("getBinaryAttributes");
method.setAccessible(true);
binaryAttributes = (SAMBinaryTagAndValue)method.invoke(mRecord);
}
catch(Exception ex) {
throw new ReviewedStingException("Unable to invoke getBinaryAttributes method",ex);
}
return binaryAttributes;
}
public List<SAMTagAndValue> getAttributes() { return mRecord.getAttributes(); }
public SAMFileHeader getHeader() { return mRecord.getHeader(); }
public void setHeader(SAMFileHeader samFileHeader) { mRecord.setHeader(samFileHeader); }
public byte[] getVariableBinaryRepresentation() { return mRecord.getVariableBinaryRepresentation(); }
public int getAttributesBinarySize() { return mRecord.getAttributesBinarySize(); }
public String format() { return mRecord.format(); }
public List<AlignmentBlock> getAlignmentBlocks() { return mRecord.getAlignmentBlocks(); }
public List<SAMValidationError> validateCigar(long l) { return mRecord.validateCigar(l); }
@Override
public boolean equals(Object o) {
if (this == o) return true;
// note -- this forbids a GATKSAMRecord being equal to its underlying SAMRecord
if (!(o instanceof GATKSAMRecord)) return false;
// note that we do not consider the GATKSAMRecord internal state at all
return mRecord.equals(((GATKSAMRecord)o).mRecord);
}
public int hashCode() { return mRecord.hashCode(); }
public List<SAMValidationError> isValid() { return mRecord.isValid(); }
public Object clone() throws CloneNotSupportedException { return mRecord.clone(); }
public String toString() { return mRecord.toString(); }
public SAMFileSource getFileSource() { return mRecord.getFileSource(); }
/**
* Sets a marker providing the source reader for this file and the position in the file from which the read originated.
* @param fileSource source of the given file.
*/
@Override
protected void setFileSource(final SAMFileSource fileSource) {
try {
Method method = SAMRecord.class.getDeclaredMethod("setFileSource",SAMFileSource.class);
method.setAccessible(true);
method.invoke(mRecord,fileSource);
}
catch(Exception ex) {
throw new ReviewedStingException("Unable to invoke setFileSource method",ex);
}
return super.equals(o);
}
}

74
public/java/src/org/broadinstitute/sting/utils/sam/GATKSamRecordFactory.java 100644
View File

@ -0,0 +1,74 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.sam;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMRecordFactory;
import net.sf.samtools.BAMRecord;
import org.broadinstitute.sting.utils.exceptions.UserException;
/**
* Factory interface implementation used to create GATKSamRecords
* from SAMFileReaders with SAM-JDK
*
* @author Mark DePristo
*/
public class GATKSamRecordFactory implements SAMRecordFactory {
/** Create a new SAMRecord to be filled in */
public SAMRecord createSAMRecord(SAMFileHeader header) {
throw new UserException.BadInput("The GATK now longer supports input SAM files");
}
/** Create a new BAM Record. */
public BAMRecord createBAMRecord(final SAMFileHeader header,
final int referenceSequenceIndex,
final int alignmentStart,
final short readNameLength,
final short mappingQuality,
final int indexingBin,
final int cigarLen,
final int flags,
final int readLen,
final int mateReferenceSequenceIndex,
final int mateAlignmentStart,
final int insertSize,
final byte[] variableLengthBlock) {
return new GATKSAMRecord(header,
referenceSequenceIndex,
alignmentStart,
readNameLength,
mappingQuality,
indexingBin,
cigarLen,
flags,
readLen,
mateReferenceSequenceIndex,
mateAlignmentStart,
insertSize,
variableLengthBlock);
}
}

32
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
View File

@ -52,38 +52,6 @@ public class ReadUtils {
// ----------------------------------------------------------------------------------------------------
public static final String REDUCED_READ_QUALITY_TAG = "RQ";
public static final String REDUCED_READ_CONSENSUS_COUNTS_TAG = "CC";
public final static byte[] getReducedReadQualityTagValue(final SAMRecord read) {
return read.getByteArrayAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
}
public final static boolean isReducedRead(final SAMRecord read) {
return getReducedReadQualityTagValue(read) != null;
}
public final static byte getReducedQual(final SAMRecord read, final int i) {
return read.getBaseQualities()[i];
}
public final static byte getReducedCount(final SAMRecord read, final int i) {
return getReducedReadQualityTagValue(read)[i];
}
public final static SAMRecord reducedReadWithReducedQuals(final SAMRecord read) {
if ( ! isReducedRead(read) ) throw new IllegalArgumentException("read must be a reduced read");
return read;
// try {
// SAMRecord newRead = (SAMRecord)read.clone();
// byte reducedQual = (byte)(int)getReducedReadQualityTagValue(read);
// byte[] newQuals = new byte[read.getBaseQualities().length];
// Arrays.fill(newQuals, reducedQual);
// newRead.setBaseQualities(newQuals);
// return newRead;
// } catch ( CloneNotSupportedException e ) {
// throw new ReviewedStingException("SAMRecord no longer supports clone", e);
// }
}
// ----------------------------------------------------------------------------------------------------
//

9
public/java/test/org/broadinstitute/sting/BaseTest.java
View File

@ -50,6 +50,7 @@ public abstract class BaseTest {
public static final String hg18Reference = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
public static final String hg19Reference = "/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta";
public static final String b36KGReference = "/humgen/1kg/reference/human_b36_both.fasta";
//public static final String b37KGReference = "/Users/depristo/Desktop/broadLocal/localData/human_g1k_v37.fasta";
public static final String b37KGReference = "/humgen/1kg/reference/human_g1k_v37.fasta";
public static final String GATKDataLocation = "/humgen/gsa-hpprojects/GATK/data/";
public static final String validationDataLocation = GATKDataLocation + "Validation_Data/";
@ -99,10 +100,10 @@ public abstract class BaseTest {
logger.setLevel(Level.WARN);
// find our file sources
if (!fileExist(hg18Reference) || !fileExist(hg19Reference) || !fileExist(b36KGReference)) {
logger.fatal("We can't locate the reference directories. Aborting!");
throw new RuntimeException("BaseTest setup failed: unable to locate the reference directories");
}
// if (!fileExist(hg18Reference) || !fileExist(hg19Reference) || !fileExist(b36KGReference)) {
// logger.fatal("We can't locate the reference directories. Aborting!");
// throw new RuntimeException("BaseTest setup failed: unable to locate the reference directories");
// }
}
/**

79
public/java/test/org/broadinstitute/sting/commandline/ArgumentMatchSiteUnitTest.java 100644
View File

@ -0,0 +1,79 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.commandline;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.io.File;
public class ArgumentMatchSiteUnitTest {
@Test
public void testCommandLine() {
ArgumentMatchSite site = new ArgumentMatchSite(ArgumentMatchSource.COMMAND_LINE, 1);
Assert.assertEquals(site.getSource(), ArgumentMatchSource.COMMAND_LINE);
Assert.assertEquals(site.getIndex(), 1);
}
@Test
public void testFile() {
ArgumentMatchSource source = new ArgumentMatchSource(new File("test"));
ArgumentMatchSite site = new ArgumentMatchSite(source, 1);
Assert.assertEquals(site.getSource(), source);
Assert.assertEquals(site.getIndex(), 1);
}
@Test
public void testEquals() {
ArgumentMatchSource cmdLine = ArgumentMatchSource.COMMAND_LINE;
ArgumentMatchSite site1 = new ArgumentMatchSite(cmdLine, 1);
ArgumentMatchSite site2 = new ArgumentMatchSite(cmdLine, 2);
Assert.assertFalse(site1.equals(null));
Assert.assertTrue(site1.equals(site1));
Assert.assertFalse(site1.equals(site2));
Assert.assertFalse(site2.equals(site1));
Assert.assertTrue(site2.equals(site2));
}
@Test
public void testCompareTo() {
ArgumentMatchSource cmdLine = ArgumentMatchSource.COMMAND_LINE;
ArgumentMatchSite site1 = new ArgumentMatchSite(cmdLine, 1);
ArgumentMatchSite site2 = new ArgumentMatchSite(cmdLine, 2);
Assert.assertTrue(site1.compareTo(site1) == 0);
Assert.assertTrue(site1.compareTo(site2) < 0);
Assert.assertTrue(site2.compareTo(site1) > 0);
Assert.assertTrue(site2.compareTo(site2) == 0);
}
@Test(expectedExceptions = NullPointerException.class)
public void testCompareToNull() {
new ArgumentMatchSite(ArgumentMatchSource.COMMAND_LINE, 0).compareTo(null);
}
}

98
public/java/test/org/broadinstitute/sting/commandline/ArgumentMatchSourceUnitTest.java 100644
View File

@ -0,0 +1,98 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.BaseTest;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.io.File;
public class ArgumentMatchSourceUnitTest extends BaseTest {
@Test
public void testCommandLine() {
ArgumentMatchSource source = ArgumentMatchSource.COMMAND_LINE;
Assert.assertEquals(source.getType(), ArgumentMatchSourceType.CommandLine);
Assert.assertNull(source.getFile());
}
@Test
public void testFile() {
File f = new File("test");
ArgumentMatchSource source = new ArgumentMatchSource(f);
Assert.assertEquals(source.getType(), ArgumentMatchSourceType.File);
Assert.assertEquals(source.getFile(), f);
}
@Test(expectedExceptions = IllegalArgumentException.class)
public void testNullFile() {
new ArgumentMatchSource(null);
}
@Test
public void testEquals() {
ArgumentMatchSource cmdLine = ArgumentMatchSource.COMMAND_LINE;
ArgumentMatchSource fileA = new ArgumentMatchSource(new File("a"));
ArgumentMatchSource fileB = new ArgumentMatchSource(new File("b"));
Assert.assertFalse(cmdLine.equals(null));
Assert.assertTrue(cmdLine.equals(cmdLine));
Assert.assertFalse(cmdLine.equals(fileA));
Assert.assertFalse(cmdLine.equals(fileB));
Assert.assertFalse(fileA.equals(cmdLine));
Assert.assertTrue(fileA.equals(fileA));
Assert.assertFalse(fileA.equals(fileB));
Assert.assertFalse(fileB.equals(cmdLine));
Assert.assertFalse(fileB.equals(fileA));
Assert.assertTrue(fileB.equals(fileB));
}
@Test
public void testCompareTo() {
ArgumentMatchSource cmdLine = ArgumentMatchSource.COMMAND_LINE;
ArgumentMatchSource fileA = new ArgumentMatchSource(new File("a"));
ArgumentMatchSource fileB = new ArgumentMatchSource(new File("b"));
Assert.assertTrue(cmdLine.compareTo(cmdLine) == 0);
Assert.assertTrue(cmdLine.compareTo(fileA) < 0);
Assert.assertTrue(cmdLine.compareTo(fileB) < 0);
Assert.assertTrue(fileA.compareTo(cmdLine) > 0);
Assert.assertTrue(fileA.compareTo(fileA) == 0);
Assert.assertTrue(fileA.compareTo(fileB) < 0);
Assert.assertTrue(fileB.compareTo(cmdLine) > 0);
Assert.assertTrue(fileB.compareTo(fileA) > 0);
Assert.assertTrue(fileB.compareTo(fileB) == 0);
}
@Test(expectedExceptions = NullPointerException.class)
public void testCompareToNull() {
ArgumentMatchSource.COMMAND_LINE.compareTo(null);
}
}

26
public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
View File

@ -25,6 +25,7 @@
package org.broadinstitute.sting.commandline;
import org.apache.commons.io.FileUtils;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@ -34,6 +35,8 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import java.io.File;
import java.io.IOException;
import java.util.List;
import java.util.EnumSet;
/**
@ -493,6 +496,7 @@ public class ParsingEngineUnitTest extends BaseTest {
Assert.assertNotNull(definition, "Invalid default argument name assigned");
}
@SuppressWarnings("unused")
private class CamelCaseArgProvider {
@Argument(doc="my arg")
Integer myArg;
@ -507,6 +511,7 @@ public class ParsingEngineUnitTest extends BaseTest {
parsingEngine.validate();
}
@SuppressWarnings("unused")
private class BooleanArgProvider {
@Argument(doc="my bool")
boolean myBool;
@ -561,6 +566,7 @@ public class ParsingEngineUnitTest extends BaseTest {
parsingEngine.validate();
}
@SuppressWarnings("unused")
private class MutuallyExclusiveArgProvider {
@Argument(doc="foo",exclusiveOf="bar")
Integer foo;
@ -618,6 +624,7 @@ public class ParsingEngineUnitTest extends BaseTest {
parsingEngine.addArgumentSource( MultipleArgumentCollectionProvider.class );
}
@SuppressWarnings("unused")
private class MultipleArgumentCollectionProvider {
@ArgumentCollection
RequiredArgProvider rap1 = new RequiredArgProvider();
@ -937,4 +944,23 @@ public class ParsingEngineUnitTest extends BaseTest {
VariantContextRodBindingArgProvider argProvider = new VariantContextRodBindingArgProvider();
parsingEngine.loadArgumentsIntoObject( argProvider );
}
@Test
public void argumentListTest() throws IOException {
File argsFile = BaseTest.createTempFile("args.", ".list");
try {
FileUtils.write(argsFile, "-I na12878.bam");
final String[] commandLine = new String[] {"-args", argsFile.getPath()};
parsingEngine.addArgumentSource(InputFileArgProvider.class);
parsingEngine.parse(commandLine);
parsingEngine.validate();
InputFileArgProvider argProvider = new InputFileArgProvider();
parsingEngine.loadArgumentsIntoObject(argProvider);
Assert.assertEquals(argProvider.inputFile, "na12878.bam", "Argument is not correctly initialized");
} finally {
FileUtils.deleteQuietly(argsFile);
}
}
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/BAQIntegrationTest.java
View File

@ -18,7 +18,7 @@ public class BAQIntegrationTest extends WalkerTest {
// --------------------------------------------------------------------------------------------------------------
@Test
public void testPrintReadsNoBAQ() {
WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF", 1, Arrays.asList("902197bf77ed5a828d50e08771685928"));
WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF", 1, Arrays.asList("d97340a2bba2c6320d1ebeb86024a27c"));
executeTest(String.format("testPrintReadsNoBAQ"), spec);
}

12
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -224,7 +224,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("0bece77ce6bc447438ef9b2921b2dc41"));
Arrays.asList("eeba568272f9b42d5450da75c7cc6d2d"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@ -252,7 +252,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("790b1a1d6ab79eee8c24812bb8ca6fae"));
Arrays.asList("19ff9bd3139480bdf79dcbf117cf2b24"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
@ -262,7 +262,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("408d3aba4d094c067fc00a43992c2292"));
Arrays.asList("118918f2e9e56a3cfc5ccb2856d529c8"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1);
}
@ -272,7 +272,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
+ validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("5e4e09354410b76fc0d822050d84132a"));
Arrays.asList("a20799237accd52c1b8c2ac096309c8f"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
}
@ -282,7 +282,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2.20101123.indels.sites.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,080,000", 1,
Arrays.asList("c599eedbeb422713b8a28529e805e4ae"));
Arrays.asList("18ef8181157b4ac3eb8492f538467f92"));
executeTest("test MultiSample Pilot2 indels with complicated records", spec3);
}
@ -291,7 +291,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec4 = new WalkerTest.WalkerTestSpec(
baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2_chr20_100_110K.20101123.indels.sites.vcf -I " + validationDataLocation +
"phase1_GBR_realigned.chr20.100K-110K.bam -o %s -L 20:100,000-110,000", 1,
Arrays.asList("37d908a682ac269f8f19dec939ff5b01"));
Arrays.asList("ad884e511a751b05e64db5314314365a"));
executeTest("test MultiSample 1000G Phase1 indels with complicated records emitting all sites", spec4);
}

46
public/java/test/org/broadinstitute/sting/utils/R/RScriptLibraryUnitTest.java 100644
View File

@ -0,0 +1,46 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.R;
import org.apache.commons.io.FileUtils;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.io.File;
public class RScriptLibraryUnitTest {
@Test
public void testProperties() {
Assert.assertEquals(RScriptLibrary.GSALIB.getLibraryName(), "gsalib");
Assert.assertEquals(RScriptLibrary.GSALIB.getResourcePath(), "gsalib.tar.gz");
}
@Test
public void testWriteTemp() {
File file = RScriptLibrary.GSALIB.writeTemp();
Assert.assertTrue(file.exists(), "R library was not written to temp file: " + file);
FileUtils.deleteQuietly(file);
}
}

12
public/java/test/org/broadinstitute/sting/utils/ReadUtilsUnitTest.java
View File

@ -5,6 +5,7 @@ import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.testng.Assert;
import org.testng.annotations.BeforeTest;
@ -12,7 +13,7 @@ import org.testng.annotations.Test;
public class ReadUtilsUnitTest extends BaseTest {
SAMRecord read, reducedRead;
GATKSAMRecord read, reducedRead;
final static String BASES = "ACTG";
final static String QUALS = "!+5?";
final private static byte[] REDUCED_READ_COUNTS = new byte[]{10, 20, 30, 40};
@ -47,13 +48,12 @@ public class ReadUtilsUnitTest extends BaseTest {
@Test
public void testReducedReads() {
Assert.assertFalse(ReadUtils.isReducedRead(read), "isReducedRead is false for normal read");
Assert.assertEquals(ReadUtils.getReducedReadQualityTagValue(read), null, "No reduced read tag in normal read");
Assert.assertFalse(read.isReducedRead(), "isReducedRead is false for normal read");
Assert.assertEquals(read.getReducedReadCounts(), null, "No reduced read tag in normal read");
Assert.assertTrue(ReadUtils.isReducedRead(reducedRead), "isReducedRead is true for reduced read");
Assert.assertTrue(reducedRead.isReducedRead(), "isReducedRead is true for reduced read");
for ( int i = 0; i < reducedRead.getReadLength(); i++) {
Assert.assertEquals(ReadUtils.getReducedQual(reducedRead, i), read.getBaseQualities()[i], "Reduced read quality not set to the expected value at " + i);
Assert.assertEquals(ReadUtils.getReducedCount(reducedRead, i), REDUCED_READ_COUNTS[i], "Reduced read count not set to the expected value at " + i);
Assert.assertEquals(reducedRead.getReducedCount(i), REDUCED_READ_COUNTS[i], "Reduced read count not set to the expected value at " + i);
}
}

5
public/java/test/org/broadinstitute/sting/utils/ReservoirDownsamplerUnitTest.java
View File

@ -1,5 +1,6 @@
package org.broadinstitute.sting.utils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.testng.Assert;
import org.testng.annotations.Test;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
@ -28,7 +29,7 @@ public class ReservoirDownsamplerUnitTest {
@Test
public void testOneElementWithPoolSizeOne() {
List<SAMRecord> reads = Collections.singletonList(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76));
List<GATKSAMRecord> reads = Collections.singletonList(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76));
ReservoirDownsampler<SAMRecord> downsampler = new ReservoirDownsampler<SAMRecord>(1);
downsampler.addAll(reads);
@ -40,7 +41,7 @@ public class ReservoirDownsamplerUnitTest {
@Test
public void testOneElementWithPoolSizeGreaterThanOne() {
List<SAMRecord> reads = Collections.singletonList(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76));
List<GATKSAMRecord> reads = Collections.singletonList(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76));
ReservoirDownsampler<SAMRecord> downsampler = new ReservoirDownsampler<SAMRecord>(5);
downsampler.addAll(reads);

197
public/java/test/org/broadinstitute/sting/utils/io/IOUtilsUnitTest.java 100644
View File

@ -0,0 +1,197 @@
package org.broadinstitute.sting.utils.io;
import org.apache.commons.io.FileUtils;
import org.broadinstitute.sting.BaseTest;
import java.io.File;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.Assert;
import org.testng.annotations.Test;
public class IOUtilsUnitTest extends BaseTest {
@Test
public void testGoodTempDir() {
IOUtils.checkTempDir(new File("/tmp/queue"));
}
@Test(expectedExceptions=UserException.BadTmpDir.class)
public void testBadTempDir() {
IOUtils.checkTempDir(new File("/tmp"));
}
@Test
public void testAbsoluteSubDir() {
File subDir = IOUtils.absolute(new File("."), new File("/path/to/file"));
Assert.assertEquals(subDir, new File("/path/to/file"));
subDir = IOUtils.absolute(new File("/different/path"), new File("/path/to/file"));
Assert.assertEquals(subDir, new File("/path/to/file"));
subDir = IOUtils.absolute(new File("/different/path"), new File("."));
Assert.assertEquals(subDir, new File("/different/path"));
}
@Test
public void testRelativeSubDir() throws IOException {
File subDir = IOUtils.absolute(new File("."), new File("path/to/file"));
Assert.assertEquals(subDir.getCanonicalFile(), new File("path/to/file").getCanonicalFile());
subDir = IOUtils.absolute(new File("/different/path"), new File("path/to/file"));
Assert.assertEquals(subDir, new File("/different/path/path/to/file"));
}
@Test
public void testDottedSubDir() throws IOException {
File subDir = IOUtils.absolute(new File("."), new File("path/../to/file"));
Assert.assertEquals(subDir.getCanonicalFile(), new File("path/../to/./file").getCanonicalFile());
subDir = IOUtils.absolute(new File("."), new File("/path/../to/file"));
Assert.assertEquals(subDir, new File("/path/../to/file"));
subDir = IOUtils.absolute(new File("/different/../path"), new File("path/to/file"));
Assert.assertEquals(subDir, new File("/different/../path/path/to/file"));
subDir = IOUtils.absolute(new File("/different/./path"), new File("/path/../to/file"));
Assert.assertEquals(subDir, new File("/path/../to/file"));
}
@Test
public void testTempDir() {
File tempDir = IOUtils.tempDir("Q-Unit-Test", "", new File("queueTempDirToDelete"));
Assert.assertTrue(tempDir.exists());
Assert.assertFalse(tempDir.isFile());
Assert.assertTrue(tempDir.isDirectory());
boolean deleted = IOUtils.tryDelete(tempDir);
Assert.assertTrue(deleted);
Assert.assertFalse(tempDir.exists());
}
@Test
public void testDirLevel() {
File dir = IOUtils.dirLevel(new File("/path/to/directory"), 1);
Assert.assertEquals(dir, new File("/path"));
dir = IOUtils.dirLevel(new File("/path/to/directory"), 2);
Assert.assertEquals(dir, new File("/path/to"));
dir = IOUtils.dirLevel(new File("/path/to/directory"), 3);
Assert.assertEquals(dir, new File("/path/to/directory"));
dir = IOUtils.dirLevel(new File("/path/to/directory"), 4);
Assert.assertEquals(dir, new File("/path/to/directory"));
}
@Test
public void testAbsolute() {
File dir = IOUtils.absolute(new File("/path/./to/./directory/."));
Assert.assertEquals(dir, new File("/path/to/directory"));
dir = IOUtils.absolute(new File("/"));
Assert.assertEquals(dir, new File("/"));
dir = IOUtils.absolute(new File("/."));
Assert.assertEquals(dir, new File("/"));
dir = IOUtils.absolute(new File("/././."));
Assert.assertEquals(dir, new File("/"));
dir = IOUtils.absolute(new File("/./directory/."));
Assert.assertEquals(dir, new File("/directory"));
dir = IOUtils.absolute(new File("/./directory/./"));
Assert.assertEquals(dir, new File("/directory"));
dir = IOUtils.absolute(new File("/./directory./"));
Assert.assertEquals(dir, new File("/directory."));
dir = IOUtils.absolute(new File("/./.directory/"));
Assert.assertEquals(dir, new File("/.directory"));
}
@Test
public void testTail() throws IOException {
List<String> lines = Arrays.asList(
"chr18_random 4262 3154410390 50 51",
"chr19_random 301858 3154414752 50 51",
"chr21_random 1679693 3154722662 50 51",
"chr22_random 257318 3156435963 50 51",
"chrX_random 1719168 3156698441 50 51");
List<String> tail = IOUtils.tail(new File(BaseTest.hg18Reference + ".fai"), 5);
Assert.assertEquals(tail.size(), 5);
for (int i = 0; i < 5; i++)
Assert.assertEquals(tail.get(i), lines.get(i));
}
@Test
public void testWriteSystemFile() throws IOException {
File temp = createTempFile("temp.", ".properties");
try {
IOUtils.writeResource(new Resource("StingText.properties", null), temp);
} finally {
FileUtils.deleteQuietly(temp);
}
}
@Test
public void testWriteSystemTempFile() throws IOException {
File temp = IOUtils.writeTempResource(new Resource("StingText.properties", null));
try {
Assert.assertTrue(temp.getName().startsWith("StingText"), "File does not start with 'StingText.': " + temp);
Assert.assertTrue(temp.getName().endsWith(".properties"), "File does not end with '.properties': " + temp);
} finally {
FileUtils.deleteQuietly(temp);
}
}
@Test(expectedExceptions = IllegalArgumentException.class)
public void testMissingSystemFile() throws IOException {
File temp = createTempFile("temp.", ".properties");
try {
IOUtils.writeResource(new Resource("MissingStingText.properties", null), temp);
} finally {
FileUtils.deleteQuietly(temp);
}
}
@Test
public void testWriteRelativeFile() throws IOException {
File temp = createTempFile("temp.", ".properties");
try {
IOUtils.writeResource(new Resource("/StingText.properties", IOUtils.class), temp);
} finally {
FileUtils.deleteQuietly(temp);
}
}
@Test
public void testWriteRelativeTempFile() throws IOException {
File temp = IOUtils.writeTempResource(new Resource("/StingText.properties", IOUtils.class));
try {
Assert.assertTrue(temp.getName().startsWith("StingText"), "File does not start with 'StingText.': " + temp);
Assert.assertTrue(temp.getName().endsWith(".properties"), "File does not end with '.properties': " + temp);
} finally {
FileUtils.deleteQuietly(temp);
}
}
@Test(expectedExceptions = IllegalArgumentException.class)
public void testMissingRelativeFile() throws IOException {
File temp = createTempFile("temp.", ".properties");
try {
// Looking for /org/broadinstitute/sting/utils/file/StingText.properties
IOUtils.writeResource(new Resource("StingText.properties", IOUtils.class), temp);
} finally {
FileUtils.deleteQuietly(temp);
}
}
@Test
public void testResourceProperties() {
Resource resource = new Resource("foo", Resource.class);
Assert.assertEquals(resource.getPath(), "foo");
Assert.assertEquals(resource.getRelativeClass(), Resource.class);
}
}

84
public/java/test/org/broadinstitute/sting/utils/pileup/FragmentPileupBenchmark.java 100644
View File

@ -0,0 +1,84 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.pileup;
import com.google.caliper.Param;
import com.google.caliper.SimpleBenchmark;
import com.google.caliper.runner.CaliperMain;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import java.util.*;
/**
* Caliper microbenchmark of fragment pileup
*/
public class FragmentPileupBenchmark extends SimpleBenchmark {
List<ReadBackedPileup> pileups;
@Param({"0", "4", "30", "150", "1000"})
int pileupSize; // set automatically by framework
@Param({"200", "400"})
int insertSize; // set automatically by framework
@Override protected void setUp() {
final int nPileupsToGenerate = 100;
pileups = new ArrayList<ReadBackedPileup>(nPileupsToGenerate);
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
GenomeLocParser genomeLocParser;
genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
GenomeLoc loc = genomeLocParser.createGenomeLoc("chr1", 50);
final int readLen = 100;
for ( int pileupN = 0; pileupN < nPileupsToGenerate; pileupN++ ) {
ReadBackedPileup rbp = ArtificialSAMUtils.createReadBackedPileup(header, loc, readLen, insertSize, pileupSize);
pileups.add(rbp);
}
}
private void run(int rep, FragmentPileup.FragmentMatchingAlgorithm algorithm) {
int nFrags = 0;
for ( int i = 0; i < rep; i++ ) {
for ( ReadBackedPileup rbp : pileups )
nFrags += new FragmentPileup(rbp, algorithm).getTwoReadPileup().size();
}
}
public void timeOriginal(int rep) {
run(rep, FragmentPileup.FragmentMatchingAlgorithm.ORIGINAL);
}
public void timeSkipNonOverlapping(int rep) {
run(rep, FragmentPileup.FragmentMatchingAlgorithm.skipNonOverlapping);
}
public static void main(String[] args) {
CaliperMain.main(FragmentPileupBenchmark.class, args);
}
}

126
public/java/test/org/broadinstitute/sting/utils/pileup/FragmentPileupUnitTest.java 100644
View File

@ -0,0 +1,126 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.pileup;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.testng.Assert;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.util.*;
/**
* Test routines for read-backed pileup.
*/
public class FragmentPileupUnitTest extends BaseTest {
private static SAMFileHeader header;
private class FragmentPileupTest extends TestDataProvider {
List<TestState> states = new ArrayList<TestState>();
private FragmentPileupTest(String name, int readLen, int leftStart, int rightStart, boolean leftIsFirst, boolean leftIsNegative) {
super(FragmentPileupTest.class, String.format("%s-leftIsFirst:%b-leftIsNegative:%b", name, leftIsFirst, leftIsNegative));
List<SAMRecord> pair = ArtificialSAMUtils.createPair(header, "readpair", readLen, leftStart, rightStart, leftIsFirst, leftIsNegative);
SAMRecord left = pair.get(0);
SAMRecord right = pair.get(1);
for ( int pos = leftStart; pos < rightStart + readLen; pos++) {
boolean posCoveredByLeft = pos >= left.getAlignmentStart() && pos <= left.getAlignmentEnd();
boolean posCoveredByRight = pos >= right.getAlignmentStart() && pos <= right.getAlignmentEnd();
if ( posCoveredByLeft || posCoveredByRight ) {
List<SAMRecord> reads = new ArrayList<SAMRecord>();
List<Integer> offsets = new ArrayList<Integer>();
if ( posCoveredByLeft ) {
reads.add(left);
offsets.add(pos - left.getAlignmentStart());
}
if ( posCoveredByRight ) {
reads.add(right);
offsets.add(pos - right.getAlignmentStart());
}
boolean shouldBeFragment = posCoveredByLeft && posCoveredByRight;
ReadBackedPileup pileup = new ReadBackedPileupImpl(null, reads, offsets);
TestState testState = new TestState(shouldBeFragment, pileup);
states.add(testState);
}
}
}
}
private class TestState {
boolean shouldBeFragment;
ReadBackedPileup pileup;
private TestState(final boolean shouldBeFragment, final ReadBackedPileup pileup) {
this.shouldBeFragment = shouldBeFragment;
this.pileup = pileup;
}
}
@DataProvider(name = "fragmentPileupTest")
public Object[][] createTests() {
for ( boolean leftIsFirst : Arrays.asList(true, false) ) {
for ( boolean leftIsNegative : Arrays.asList(true, false) ) {
// Overlapping pair
// ----> [first]
// <--- [second]
new FragmentPileupTest("overlapping-pair", 10, 1, 5, leftIsFirst, leftIsNegative);
// Non-overlapping pair
// ---->
// <----
new FragmentPileupTest("nonoverlapping-pair", 10, 1, 15, leftIsFirst, leftIsNegative);
}
}
return FragmentPileupTest.getTests(FragmentPileupTest.class);
}
@Test(enabled = true, dataProvider = "fragmentPileupTest")
public void testMe(FragmentPileupTest test) {
for ( TestState testState : test.states ) {
ReadBackedPileup rbp = testState.pileup;
FragmentPileup fp = new FragmentPileup(rbp);
Assert.assertEquals(fp.getTwoReadPileup().size(), testState.shouldBeFragment ? 1 : 0);
Assert.assertEquals(fp.getOneReadPileup().size(), testState.shouldBeFragment ? 0 : 1);
}
}
@BeforeTest
public void setup() {
header = ArtificialSAMUtils.createArtificialSamHeader(1,1,1000);
}
}

517
public/java/test/org/broadinstitute/sting/utils/runtime/ProcessControllerUnitTest.java 100644
View File

@ -0,0 +1,517 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.runtime;
import org.apache.commons.io.FileUtils;
import org.apache.commons.lang.StringUtils;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.io.IOUtils;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.File;
import java.io.IOException;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
public class ProcessControllerUnitTest extends BaseTest {
private static final String NL = String.format("%n");
@Test(timeOut = 60 * 1000)
public void testDestroyThreadLocal() throws InterruptedException {
for (int i = 0; i < 3; i++) {
final ProcessController controller = ProcessController.getThreadLocal();
final ProcessSettings job = new ProcessSettings(
new String[] {"sh", "-c", "echo Hello World && sleep 600 && echo Goodbye"});
job.getStdoutSettings().setBufferSize(-1);
Thread t = new Thread(new Runnable() {
@Override
public void run() {
System.out.println("BACK: Starting on background thread");
ProcessOutput result = controller.exec(job);
// Assert in background thread doesn't make it to main thread but does print a trace.
Assert.assertTrue(result.getExitValue() != 0, "Destroy-attempted job returned zero exit status");
System.out.println("BACK: Background thread exiting");
}
});
System.out.println("MAIN: Starting background thread");
t.start();
System.out.println("MAIN: Sleeping main thread 3s");
Thread.sleep(3000);
System.out.println("MAIN: Destroying job");
controller.tryDestroy();
System.out.println("MAIN: Not waiting on background thread to exit");
// Using standard java.io this was blocking on linux.
// TODO: try again with NIO.
//t.join();
//System.out.println("MAIN: Background thread exited");
}
}
@Test
public void testReuseAfterError() {
ProcessController controller = new ProcessController();
ProcessSettings job;
for (int i = 0; i < 3; i++) {
// Test bad command
job = new ProcessSettings(new String[] {"no_such_command"});
try {
controller.exec(job);
} catch (ReviewedStingException e) {
/* Was supposed to throw an exception */
}
// Test exit != 0
job = new ProcessSettings(new String[] {"cat", "non_existent_file"});
int exitValue = controller.exec(job).getExitValue();
Assert.assertTrue(exitValue != 0, "'cat' non existent file returned 0");
// Text success
job = new ProcessSettings(new String[] {"echo", "Hello World"});
exitValue = controller.exec(job).getExitValue();
Assert.assertEquals(exitValue, 0, "Echo failed");
}
}
@Test
public void testEnvironment() {
String key = "MY_NEW_VAR";
String value = "value is here";
ProcessSettings job = new ProcessSettings(new String[] {"sh", "-c", "echo $"+key});
job.getStdoutSettings().setBufferSize(-1);
job.setRedirectErrorStream(true);
Map<String, String> env = new HashMap<String, String>(System.getenv());
env.put(key, value);
job.setEnvironment(env);
ProcessController controller = new ProcessController();
ProcessOutput result = controller.exec(job);
int exitValue = result.getExitValue();
Assert.assertEquals(exitValue, 0, "Echo environment variable failed");
Assert.assertEquals(result.getStdout().getBufferString(), value + NL, "Echo environment returned unexpected output");
}
@Test
public void testDirectory() throws IOException {
File dir = null;
try {
dir = IOUtils.tempDir("temp.", "").getCanonicalFile();
ProcessSettings job = new ProcessSettings(new String[] {"pwd"});
job.getStdoutSettings().setBufferSize(-1);
job.setRedirectErrorStream(true);
job.setDirectory(dir);
ProcessController controller = new ProcessController();
ProcessOutput result = controller.exec(job);
int exitValue = result.getExitValue();
Assert.assertEquals(exitValue, 0, "Getting working directory failed");
Assert.assertEquals(result.getStdout().getBufferString(), dir.getAbsolutePath() + NL,
"Setting/getting working directory returned unexpected output");
} finally {
FileUtils.deleteQuietly(dir);
}
}
@Test
public void testReadStdInBuffer() {
String bufferText = "Hello from buffer";
ProcessSettings job = new ProcessSettings(new String[] {"cat"});
job.getStdoutSettings().setBufferSize(-1);
job.setRedirectErrorStream(true);
job.getStdinSettings().setInputBuffer(bufferText);
ProcessController controller = new ProcessController();
ProcessOutput output = controller.exec(job);
Assert.assertEquals(output.getStdout().getBufferString(), bufferText,
"Unexpected output from cat stdin buffer");
}
@Test
public void testReadStdInFile() {
File input = null;
try {
String fileText = "Hello from file";
input = IOUtils.writeTempFile(fileText, "stdin.", ".txt", null);
ProcessSettings job = new ProcessSettings(new String[] {"cat"});
job.getStdoutSettings().setBufferSize(-1);
job.setRedirectErrorStream(true);
job.getStdinSettings().setInputFile(input);
ProcessController controller = new ProcessController();
ProcessOutput output = controller.exec(job);
Assert.assertEquals(output.getStdout().getBufferString(), fileText,
"Unexpected output from cat stdin file");
} finally {
FileUtils.deleteQuietly(input);
}
}
@Test
public void testWriteStdOut() {
ProcessSettings job = new ProcessSettings(new String[] {"echo", "Testing to stdout"});
// Not going to call the System.setOut() for now. Just running a basic visual test.
job.getStdoutSettings().printStandard(true);
job.setRedirectErrorStream(true);
System.out.println("testWriteStdOut: Writing two lines to std out...");
ProcessController controller = new ProcessController();
controller.exec(job);
job.setCommand(new String[]{"cat", "non_existent_file"});
controller.exec(job);
System.out.println("testWriteStdOut: ...two lines should have been printed to std out");
}
@Test
public void testErrorToOut() throws IOException {
File outFile = null;
File errFile = null;
try {
outFile = BaseTest.createTempFile("temp", "");
errFile = BaseTest.createTempFile("temp", "");
ProcessSettings job = new ProcessSettings(new String[]{"cat", "non_existent_file"});
job.getStdoutSettings().setOutputFile(outFile);
job.getStdoutSettings().setBufferSize(-1);
job.getStderrSettings().setOutputFile(errFile);
job.getStderrSettings().setBufferSize(-1);
job.setRedirectErrorStream(true);
ProcessOutput result = new ProcessController().exec(job);
int exitValue = result.getExitValue();
Assert.assertTrue(exitValue != 0, "'cat' non existent file returned 0");
String fileString, bufferString;
fileString = FileUtils.readFileToString(outFile);
Assert.assertTrue(fileString.length() > 0, "Out file was length 0");
bufferString = result.getStdout().getBufferString();
Assert.assertTrue(bufferString.length() > 0, "Out buffer was length 0");
Assert.assertFalse(result.getStdout().isBufferTruncated(), "Out buffer was truncated");
Assert.assertEquals(bufferString.length(), fileString.length(), "Out buffer length did not match file length");
fileString = FileUtils.readFileToString(errFile);
Assert.assertEquals(fileString, "", "Unexpected output to err file");
bufferString = result.getStderr().getBufferString();
Assert.assertEquals(bufferString, "", "Unexepected output to err buffer");
} finally {
FileUtils.deleteQuietly(outFile);
FileUtils.deleteQuietly(errFile);
}
}
@Test
public void testErrorToErr() throws IOException {
File outFile = null;
File errFile = null;
try {
outFile = BaseTest.createTempFile("temp", "");
errFile = BaseTest.createTempFile("temp", "");
ProcessSettings job = new ProcessSettings(new String[]{"cat", "non_existent_file"});
job.getStdoutSettings().setOutputFile(outFile);
job.getStdoutSettings().setBufferSize(-1);
job.getStderrSettings().setOutputFile(errFile);
job.getStderrSettings().setBufferSize(-1);
job.setRedirectErrorStream(false);
ProcessOutput result = new ProcessController().exec(job);
int exitValue = result.getExitValue();
Assert.assertTrue(exitValue != 0, "'cat' non existent file returned 0");
String fileString, bufferString;
fileString = FileUtils.readFileToString(errFile);
Assert.assertTrue(fileString.length() > 0, "Err file was length 0");
bufferString = result.getStderr().getBufferString();
Assert.assertTrue(bufferString.length() > 0, "Err buffer was length 0");
Assert.assertFalse(result.getStderr().isBufferTruncated(), "Err buffer was truncated");
Assert.assertEquals(bufferString.length(), fileString.length(), "Err buffer length did not match file length");
fileString = FileUtils.readFileToString(outFile);
Assert.assertEquals(fileString, "", "Unexpected output to out file");
bufferString = result.getStdout().getBufferString();
Assert.assertEquals(bufferString, "", "Unexepected output to out buffer");
} finally {
FileUtils.deleteQuietly(outFile);
FileUtils.deleteQuietly(errFile);
}
}
private static final String TRUNCATE_TEXT = "Hello World";
private static final byte[] TRUNCATE_OUTPUT_BYTES = (TRUNCATE_TEXT + NL).getBytes();
/**
* @return Test truncating content vs. not truncating (run at -1/+1 size)
*/
@DataProvider(name = "truncateSizes")
public Object[][] getTruncateBufferSizes() {
int l = TRUNCATE_OUTPUT_BYTES.length;
return new Object[][]{
new Object[]{0, 0},
new Object[]{l, l},
new Object[]{l + 1, l},
new Object[]{l - 1, l - 1}
};
}
@Test(dataProvider = "truncateSizes")
public void testTruncateBuffer(int truncateLen, int expectedLen) {
byte[] expected = Arrays.copyOf(TRUNCATE_OUTPUT_BYTES, expectedLen);
String[] command = {"echo", TRUNCATE_TEXT};
ProcessController controller = new ProcessController();
ProcessSettings job = new ProcessSettings(command);
job.getStdoutSettings().setBufferSize(truncateLen);
ProcessOutput result = controller.exec(job);
int exitValue = result.getExitValue();
Assert.assertEquals(exitValue, 0,
String.format("Echo returned %d: %s", exitValue, TRUNCATE_TEXT));
byte[] bufferBytes = result.getStdout().getBufferBytes();
Assert.assertEquals(bufferBytes, expected,
String.format("Output buffer didn't match (%d vs %d)", expected.length, bufferBytes.length));
boolean truncated = result.getStdout().isBufferTruncated();
Assert.assertEquals(truncated, TRUNCATE_OUTPUT_BYTES.length > truncateLen,
"Unexpected buffer truncation result");
}
private static final String[] LONG_COMMAND = getLongCommand();
private static final String LONG_COMMAND_STRING = StringUtils.join(LONG_COMMAND, " ");
private static final String LONG_COMMAND_DESCRIPTION = "<long command>";
@DataProvider(name = "echoCommands")
public Object[][] getEchoCommands() {
new EchoCommand(new String[]{"echo", "Hello", "World"}, "Hello World" + NL);
new EchoCommand(new String[]{"echo", "'Hello", "World"}, "'Hello World" + NL);
new EchoCommand(new String[]{"echo", "Hello", "World'"}, "Hello World'" + NL);
new EchoCommand(new String[]{"echo", "'Hello", "World'"}, "'Hello World'" + NL);
String[] longCommand = new String[LONG_COMMAND.length + 1];
longCommand[0] = "echo";
System.arraycopy(LONG_COMMAND, 0, longCommand, 1, LONG_COMMAND.length);
new EchoCommand(longCommand, LONG_COMMAND_STRING + NL) {
@Override
public String toString() {
return LONG_COMMAND_DESCRIPTION;
}
};
return TestDataProvider.getTests(EchoCommand.class);
}
@Test(dataProvider = "echoCommands")
public void testEcho(EchoCommand script) throws IOException {
File outputFile = null;
try {
outputFile = BaseTest.createTempFile("temp", "");
ProcessSettings job = new ProcessSettings(script.command);
if (script.output != null) {
job.getStdoutSettings().setOutputFile(outputFile);
job.getStdoutSettings().setBufferSize(script.output.getBytes().length);
}
ProcessOutput result = new ProcessController().exec(job);
int exitValue = result.getExitValue();
Assert.assertEquals(exitValue, 0,
String.format("Echo returned %d: %s", exitValue, script));
if (script.output != null) {
String fileString = FileUtils.readFileToString(outputFile);
Assert.assertEquals(fileString, script.output,
String.format("Output file didn't match (%d vs %d): %s",
fileString.length(), script.output.length(), script));
String bufferString = result.getStdout().getBufferString();
Assert.assertEquals(bufferString, script.output,
String.format("Output content didn't match (%d vs %d): %s",
bufferString.length(), script.output.length(), script));
Assert.assertFalse(result.getStdout().isBufferTruncated(),
"Output content was truncated: " + script);
}
} finally {
FileUtils.deleteQuietly(outputFile);
}
}
@Test(expectedExceptions = ReviewedStingException.class)
public void testUnableToStart() {
ProcessSettings job = new ProcessSettings(new String[]{"no_such_command"});
new ProcessController().exec(job);
}
@DataProvider(name = "scriptCommands")
public Object[][] getScriptCommands() {
new ScriptCommand(true, "echo Hello World", "Hello World" + NL);
new ScriptCommand(false, "echo 'Hello World", null);
new ScriptCommand(false, "echo Hello World'", null);
new ScriptCommand(true, "echo 'Hello World'", "Hello World" + NL);
new ScriptCommand(true, "echo \"Hello World\"", "Hello World" + NL);
new ScriptCommand(false, "no_such_echo Hello World", null);
new ScriptCommand(true, "echo #", NL);
new ScriptCommand(true, "echo \\#", "#" + NL);
new ScriptCommand(true, "echo \\\\#", "\\#" + NL);
new ScriptCommand(true, "echo " + LONG_COMMAND_STRING, LONG_COMMAND_STRING + NL) {
@Override
public String toString() {
return LONG_COMMAND_DESCRIPTION;
}
};
return TestDataProvider.getTests(ScriptCommand.class);
}
@Test(dataProvider = "scriptCommands")
public void testScript(ScriptCommand script) throws IOException {
File scriptFile = null;
File outputFile = null;
try {
scriptFile = writeScript(script.content);
outputFile = BaseTest.createTempFile("temp", "");
ProcessSettings job = new ProcessSettings(new String[]{"sh", scriptFile.getAbsolutePath()});
if (script.output != null) {
job.getStdoutSettings().setOutputFile(outputFile);
job.getStdoutSettings().setBufferSize(script.output.getBytes().length);
}
ProcessOutput result = new ProcessController().exec(job);
int exitValue = result.getExitValue();
Assert.assertEquals(exitValue == 0, script.succeed,
String.format("Script returned %d: %s", exitValue, script));
if (script.output != null) {
String fileString = FileUtils.readFileToString(outputFile);
Assert.assertEquals(fileString, script.output,
String.format("Output file didn't match (%d vs %d): %s",
fileString.length(), script.output.length(), script));
String bufferString = result.getStdout().getBufferString();
Assert.assertEquals(bufferString, script.output,
String.format("Output content didn't match (%d vs %d): %s",
bufferString.length(), script.output.length(), script));
Assert.assertFalse(result.getStdout().isBufferTruncated(),
"Output content was truncated: " + script);
}
} finally {
FileUtils.deleteQuietly(scriptFile);
FileUtils.deleteQuietly(outputFile);
}
}
private static String[] getLongCommand() {
// This command fails on some systems with a 4096 character limit when run via the old sh -c "echo ...",
// but works on the same systems when run via sh <script>
int cnt = 500;
String[] command = new String[cnt];
for (int i = 1; i <= cnt; i++) {
command[i - 1] = String.format("%03d______", i);
}
return command;
}
private static File writeScript(String contents) {
try {
File file = BaseTest.createTempFile("temp", "");
FileUtils.writeStringToFile(file, contents);
return file;
} catch (IOException e) {
throw new UserException.BadTmpDir(e.getMessage());
}
}
private static class EchoCommand extends TestDataProvider {
public final String[] command;
public final String output;
public EchoCommand(String[] command, String output) {
super(EchoCommand.class);
this.command = command;
this.output = output;
}
@Override
public String toString() {
return StringUtils.join(command, " ");
}
}
public static class ScriptCommand extends TestDataProvider {
public final boolean succeed;
public final String content;
public final String output;
public ScriptCommand(boolean succeed, String content, String output) {
super(ScriptCommand.class);
this.succeed = succeed;
this.content = content;
this.output = output;
}
@Override
public String toString() {
return content;
}
}
}

64
public/java/test/org/broadinstitute/sting/utils/variantcontext/VCFJarClassLoadingUnitTest.java
View File

@ -28,8 +28,8 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.testng.annotations.Test;
import java.io.File;
import java.io.FileNotFoundException;
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URL;
import java.net.URLClassLoader;
@ -39,10 +39,16 @@ import java.net.URLClassLoader;
public class VCFJarClassLoadingUnitTest {
@Test
public void testVCFJarClassLoading() throws ClassNotFoundException, MalformedURLException {
URI vcfURI = new File("dist/vcf.jar").toURI();
URI tribbleURI = getTribbleJarFile().toURI();
URL[] jarURLs;
ClassLoader classLoader = new URLClassLoader(new URL[] {vcfURI.toURL(),tribbleURI.toURL()}, null);
try {
jarURLs = new URL[] { getVCFJarFile().toURI().toURL(), getTribbleJarFile().toURI().toURL() };
}
catch ( FileNotFoundException e ) {
throw new ReviewedStingException("Could not find the VCF jar and/or its dependencies", e);
}
ClassLoader classLoader = new URLClassLoader(jarURLs, null);
classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.VariantContext");
classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCFCodec");
classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec");
@ -51,19 +57,49 @@ public class VCFJarClassLoadingUnitTest {
}
/**
* A very unsafe way of determining the current location of the Tribble jar file. Assumes that
* the tribble jar (as opposed to the constituent tribble classes) is on the classpath.
* Locates the tribble jar within the dist directory.
*
* This method might or might not work when built via IntelliJ's debugger.
* Makes the horrible assumption that tests will always be run from the root of a Sting clone,
* but this is much less problematic than using the classpath to locate tribble, since
* the classpath won't explicitly contain tribble when we're testing the fully-packaged
* GATK jar.
*
* @return The file representing the tribble jar.
* @return The tribble jar file, if found
* @throws FileNotFoundException If we couldn't locate a tribble jar within the dist directory
*/
private File getTribbleJarFile() {
String[] classPath = System.getProperty("java.class.path").split(File.pathSeparator);
for(String classPathEntry: classPath) {
if(classPathEntry.contains("tribble"))
return new File(classPathEntry);
private File getTribbleJarFile() throws FileNotFoundException {
File distDir = new File("dist");
if ( ! distDir.isDirectory() ) {
throw new FileNotFoundException("The dist directory does not exist");
}
throw new ReviewedStingException("Unable to find Tribble jar file");
for ( File distDirEntry : distDir.listFiles() ) {
if ( distDirEntry.getName().startsWith("tribble") && distDirEntry.getName().endsWith(".jar") ) {
return distDirEntry;
}
}
throw new FileNotFoundException("Could not find a tribble jar file in the dist directory.");
}
/**
* Locates the vcf jar within the dist directory.
*
* Makes the horrible assumption that tests will always be run from the root of a Sting clone,
* but this is much less problematic than using the classpath to locate vcf.jar, since
* the classpath won't explicitly contain vcf.jar when we're testing the fully-packaged
* GATK jar.
*
* @return The vcf jar file, if found
* @throws FileNotFoundException If we couldn't locate a vcf jar within the dist directory
*/
private File getVCFJarFile() throws FileNotFoundException {
File vcfJar = new File("dist/vcf.jar");
if ( ! vcfJar.exists() ) {
throw new FileNotFoundException("Could not find dist/vcf.jar");
}
return vcfJar;
}
}

20
public/packages/CreatePackager.xsl
View File

@ -179,13 +179,19 @@
</xsl:when>
</xsl:choose>
</xsl:for-each>
<xsl:for-each select="dir">
<fileset dir="{$staging.dir}">
<xsl:attribute name="includes">
<xsl:value-of select="concat(@name,'/**')"/>
</xsl:attribute>
</fileset>
</xsl:for-each>
<xsl:for-each select="dir">
<xsl:variable name="includes">
<xsl:choose>
<xsl:when test="@includes = ''">
<xsl:value-of select="concat(@name,'/**')"/>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="concat(@name,'/',@includes)"/>
</xsl:otherwise>
</xsl:choose>
</xsl:variable>
<fileset dir="{$staging.dir}" includes="{$includes}"/>
</xsl:for-each>
</xsl:template>
<!-- Determine the short name (filename w/o directory structure of the given filename -->

2
public/packages/GATKEngine.xml
View File

@ -32,6 +32,8 @@
<package name="org.broad.tribble.**" />
<!-- Workaround - depend on the logger impl required by JEXL -->
<package name="org.apache.commons.logging.impl" />
<!-- R packages -->
<dir name="org/broadinstitute/sting/utils/R" includes="*.tar.gz" />
</dependencies>
</executable>
<resources>

4
public/packages/Queue.xml
View File

@ -65,6 +65,10 @@
<package name="ca.mcgill.mcb.pcingola.**" />
<file path="snpEff_genes.ftl" />
<file path="snpEff_summary.ftl" />
<!-- R scripts -->
<dir name="org/broadinstitute/sting/queue" includes="**/*.R" />
</dependencies>
<modules>
<module file="GATKEngine.xml"/>

26
public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
View File

@ -33,6 +33,7 @@ import org.broadinstitute.sting.queue.engine.{QGraphSettings, QGraph}
import collection.JavaConversions._
import org.broadinstitute.sting.utils.classloader.PluginManager
import org.broadinstitute.sting.utils.exceptions.UserException
import org.broadinstitute.sting.utils.io.IOUtils
/**
* Entry point of Queue. Compiles and runs QScripts passed in to the command line.
@ -48,7 +49,6 @@ object QCommandLine extends Logging {
val shutdownHook = new Thread {
override def run() {
logger.info("Shutting down jobs. Please wait...")
ProcessController.shutdown()
qCommandLine.shutdown()
}
}
@ -56,8 +56,12 @@ object QCommandLine extends Logging {
Runtime.getRuntime.addShutdownHook(shutdownHook)
try {
CommandLineProgram.start(qCommandLine, argv);
Runtime.getRuntime.removeShutdownHook(shutdownHook)
CommandLineProgram.start(qCommandLine, argv)
try {
Runtime.getRuntime.removeShutdownHook(shutdownHook)
} catch {
case _ => /* ignore, example 'java.lang.IllegalStateException: Shutdown in progress' */
}
if (CommandLineProgram.result != 0)
System.exit(CommandLineProgram.result);
} catch {
@ -80,6 +84,7 @@ class QCommandLine extends CommandLineProgram with Logging {
private val qScriptManager = new QScriptManager
private val qGraph = new QGraph
private var qScriptClasses: File = _
private var shuttingDown = false
private lazy val pluginManager = {
qScriptClasses = IOUtils.tempDir("Q-Classes", "", settings.qSettings.tempDirectory)
@ -118,10 +123,16 @@ class QCommandLine extends CommandLineProgram with Logging {
script.onExecutionDone(qGraph.getFunctionsAndStatus(script.functions), qGraph.success)
if ( ! settings.disableJobReport ) {
val jobStringName = (QScriptUtils.?(settings.jobReportFile)).getOrElse(settings.qSettings.jobNamePrefix + ".jobreport.txt")
val jobReportFile = new File(jobStringName)
logger.info("Writing JobLogging GATKReport to file " + jobReportFile)
QJobReport.printReport(qGraph.getFunctionsAndStatus(script.functions), jobReportFile)
QJobReport.plotReport(settings.rScriptArgs, jobReportFile)
if (!shuttingDown) {
val reportFile = new File(jobStringName)
logger.info("Writing JobLogging GATKReport to file " + reportFile)
QJobReport.printReport(qGraph.getFunctionsAndStatus(script.functions), reportFile)
val pdfFile = new File(jobStringName + ".pdf")
logger.info("Plotting JobLogging GATKReport to file " + pdfFile)
QJobReport.plotReport(settings.rScriptArgs, reportFile, pdfFile)
}
}
}
@ -163,6 +174,7 @@ class QCommandLine extends CommandLineProgram with Logging {
Arrays.asList(new ScalaCompoundArgumentTypeDescriptor)
def shutdown() = {
shuttingDown = true
qGraph.shutdown()
if (qScriptClasses != null) IOUtils.tryDelete(qScriptClasses)
}

16
public/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala
View File

@ -2,7 +2,7 @@ package org.broadinstitute.sting.queue
import scala.tools.nsc.{Global, Settings}
import scala.tools.nsc.io.PlainFile
import org.broadinstitute.sting.queue.util.{Logging, IOUtils}
import org.broadinstitute.sting.queue.util.Logging
import collection.JavaConversions._
import java.io.File
import scala.tools.nsc.reporters.AbstractReporter
@ -20,7 +20,7 @@ class QScriptManager() extends Logging {
* Compiles and loads the scripts in the files into the current classloader.
* Heavily based on scala/src/compiler/scala/tools/ant/Scalac.scala
*/
def loadScripts(scripts: List[File], tempDir: File) = {
def loadScripts(scripts: List[File], tempDir: File) {
if (scripts.size > 0) {
val settings = new Settings((error: String) => logger.error(error))
settings.deprecation.value = true
@ -63,7 +63,7 @@ object QScriptManager extends Logging {
* Heavily based on scala/src/compiler/scala/tools/nsc/reporters/ConsoleReporter.scala
*/
private class Log4JReporter(val settings: Settings) extends AbstractReporter {
def displayPrompt = throw new UnsupportedOperationException("Unable to prompt the user. Prompting should be off.")
def displayPrompt { throw new UnsupportedOperationException("Unable to prompt the user. Prompting should be off.") }
/**
* Displays the message at position with severity.
@ -71,7 +71,7 @@ object QScriptManager extends Logging {
* @param msg Message to display.
* @param severity Severity of the event.
*/
def display(posIn: Position, msg: String, severity: Severity) = {
def display(posIn: Position, msg: String, severity: Severity) {
severity.count += 1
val level = severity match {
case INFO => Level.INFO
@ -87,7 +87,6 @@ object QScriptManager extends Logging {
case NoPosition =>
printMessage(level, msg)
case _ =>
val buf = new StringBuilder(msg)
val file = pos.source.file
printMessage(level, file.name+":"+pos.line+": "+msg)
printSourceLine(level, pos)
@ -97,7 +96,7 @@ object QScriptManager extends Logging {
/**
* Prints a summary count of warnings and errors.
*/
def printSummary() = {
def printSummary() {
if (WARNING.count > 0)
printMessage(Level.WARN, countElementsAsString(WARNING.count, "warning") + " found")
if (ERROR.count > 0)
@ -119,15 +118,16 @@ object QScriptManager extends Logging {
* @param level Severity level.
* @param pos Position in the file of the event.
*/
private def printColumnMarker(level: Level, pos: Position) =
private def printColumnMarker(level: Level, pos: Position) {
if (pos.isDefined) { printMessage(level, " " * (pos.column - 1) + "^") }
}
/**
* Prints the message at the severity level.
* @param level Severity level.
* @param message Message content.
*/
private def printMessage(level: Level, message: String) = {
private def printMessage(level: Level, message: String) {
logger.log(level, message)
}
}

5
public/scala/src/org/broadinstitute/sting/queue/engine/CommandLineJobRunner.scala
View File

@ -26,7 +26,8 @@ package org.broadinstitute.sting.queue.engine
import org.broadinstitute.sting.queue.function.CommandLineFunction
import java.io.File
import org.broadinstitute.sting.queue.util.{Logging, IOUtils}
import org.broadinstitute.sting.queue.util.Logging
import org.broadinstitute.sting.utils.io.IOUtils
/**
* Runs a command line function.
@ -69,7 +70,7 @@ trait CommandLineJobRunner extends JobRunner[CommandLineFunction] with Logging {
override def init() {
super.init()
var exec = new StringBuilder
val exec = new StringBuilder
var dirs = Set.empty[File]
for (dir <- function.jobDirectories)

20
public/scala/src/org/broadinstitute/sting/queue/engine/FunctionEdge.scala
View File

@ -2,7 +2,10 @@ package org.broadinstitute.sting.queue.engine
import org.broadinstitute.sting.queue.function.QFunction
import java.io.{StringWriter, PrintWriter}
import org.broadinstitute.sting.queue.util.{Logging, IOUtils}
import org.broadinstitute.sting.queue.util.Logging
import org.broadinstitute.sting.utils.io.IOUtils
import org.apache.commons.io.FileUtils
import org.apache.commons.lang.StringUtils
/**
* An edge in the QGraph that runs a QFunction.
@ -150,26 +153,19 @@ class FunctionEdge(val function: QFunction, val inputs: QNode, val outputs: QNod
/**
* Outputs the last lines of the error logs.
*/
private def tailError() = {
private def tailError() {
val errorFile = functionErrorFile
if (IOUtils.waitFor(errorFile, 120)) {
val maxLines = 100
val tailLines = IOUtils.tail(errorFile, maxLines)
val nl = "%n".format()
val summary = if (tailLines.size > maxLines) "Last %d lines".format(maxLines) else "Contents"
logger.error("%s of %s:%n%s".format(summary, errorFile, tailLines.mkString(nl)))
logger.error("%s of %s:%n%s".format(summary, errorFile, StringUtils.join(tailLines, nl)))
} else {
logger.error("Unable to access log file: %s".format(errorFile))
}
}
/**
* Writes the contents of the error to the error file.
*/
private def writeError(content: String) {
IOUtils.writeContents(functionErrorFile, content)
}
/**
* Writes the stack trace to the error file.
*/
@ -178,8 +174,8 @@ class FunctionEdge(val function: QFunction, val inputs: QNode, val outputs: QNod
val printWriter = new PrintWriter(stackTrace)
printWriter.println(function.description)
e.printStackTrace(printWriter)
printWriter.close
IOUtils.writeContents(functionErrorFile, stackTrace.toString)
printWriter.close()
FileUtils.writeStringToFile(functionErrorFile, stackTrace.toString)
}
def getRunInfo = {

6
public/scala/src/org/broadinstitute/sting/queue/engine/InProcessRunner.scala
View File

@ -2,8 +2,8 @@ package org.broadinstitute.sting.queue.engine
import org.broadinstitute.sting.queue.function.InProcessFunction
import java.util.Date
import org.broadinstitute.sting.queue.util.{Logging, IOUtils}
import org.broadinstitute.sting.utils.Utils
import org.apache.commons.io.FileUtils
/**
* Runs a function that executes in process and does not fork out an external process.
@ -11,7 +11,7 @@ import org.broadinstitute.sting.utils.Utils
class InProcessRunner(val function: InProcessFunction) extends JobRunner[InProcessFunction] {
private var runStatus: RunnerStatus.Value = _
def start() = {
def start() {
getRunInfo.startTime = new Date()
getRunInfo.exechosts = Utils.resolveHostname()
runStatus = RunnerStatus.RUNNING
@ -20,7 +20,7 @@ class InProcessRunner(val function: InProcessFunction) extends JobRunner[InProce
getRunInfo.doneTime = new Date()
val content = "%s%nDone.".format(function.description)
IOUtils.writeContents(function.jobOutputFile, content)
FileUtils.writeStringToFile(function.jobOutputFile, content)
runStatus = RunnerStatus.DONE
}

24
public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
View File

@ -40,6 +40,7 @@ import collection.immutable.{TreeSet, TreeMap}
import org.broadinstitute.sting.queue.function.scattergather.{ScatterFunction, CloneFunction, GatherFunction, ScatterGatherableFunction}
import java.util.Date
import org.broadinstitute.sting.utils.Utils
import org.broadinstitute.sting.utils.io.IOUtils
/**
* The internal dependency tracker between sets of function input and output files.
@ -416,8 +417,12 @@ class QGraph extends Logging {
startedJobsToEmail = Set.empty[FunctionEdge]
}
if (readyJobs.size == 0 && runningJobs.size > 0)
Thread.sleep(nextRunningCheck(lastRunningCheck))
if (readyJobs.size == 0 && runningJobs.size > 0) {
runningLock.synchronized {
if (running)
runningLock.wait(nextRunningCheck(lastRunningCheck))
}
}
lastRunningCheck = System.currentTimeMillis
updateStatus()
@ -1002,7 +1007,12 @@ class QGraph extends Logging {
true
} else {
!this.jobGraph.edgeSet.exists(edge => {
edge.isInstanceOf[FunctionEdge] && edge.asInstanceOf[FunctionEdge].status == RunnerStatus.FAILED
if (edge.isInstanceOf[FunctionEdge]) {
val status = edge.asInstanceOf[FunctionEdge].status
(status == RunnerStatus.PENDING || status == RunnerStatus.RUNNING || status == RunnerStatus.FAILED)
} else {
false
}
})
}
}
@ -1051,7 +1061,13 @@ class QGraph extends Logging {
def shutdown() {
// Signal the main thread to shutdown.
running = false
// Wait for the thread to finish and exit normally.
// Try and wait for the thread to finish and exit normally.
runningLock.synchronized {
runningLock.notify()
}
// Start killing jobs.
runningLock.synchronized {
val runners = runningJobs.map(_.runner)
runningJobs = Set.empty[FunctionEdge]

2
public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobManager.scala
View File

@ -56,6 +56,6 @@ class DrmaaJobManager extends CommandLineJobManager[DrmaaJobRunner] {
updatedRunners
}
override def tryStop(runners: Set[DrmaaJobRunner]) {
runners.filterNot(_.jobId == null).foreach(_.tryStop())
runners.foreach(_.tryStop())
}
}

20
public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala
View File

@ -135,14 +135,18 @@ class DrmaaJobRunner(val session: Session, val function: CommandLineFunction) ex
def tryStop() {
session.synchronized {
try {
// Stop runners. SIGTERM(15) is preferred to SIGKILL(9).
// Only way to send SIGTERM is for the Sys Admin set the terminate_method
// resource of the designated queue to SIGTERM
session.control(jobId, Session.TERMINATE)
} catch {
case e =>
logger.error("Unable to kill job " + jobId, e)
// Assumes that after being set the job may be
// reassigned but will not be reset back to null
if (jobId != null) {
try {
// Stop runners. SIGTERM(15) is preferred to SIGKILL(9).
// Only way to send SIGTERM is for the Sys Admin set the terminate_method
// resource of the designated queue to SIGTERM
session.control(jobId, Session.TERMINATE)
} catch {
case e =>
logger.error("Unable to kill job " + jobId, e)
}
}
}
}

1
public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobManager.scala
View File

@ -30,4 +30,5 @@ import org.broadinstitute.sting.queue.engine.CommandLineJobManager
class ShellJobManager extends CommandLineJobManager[ShellJobRunner] {
def runnerType = classOf[ShellJobRunner]
def create(function: CommandLineFunction) = new ShellJobRunner(function)
override def tryStop(runners: Set[ShellJobRunner]) { runners.foreach(_.tryStop()) }
}

51
public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala
View File

@ -25,41 +25,66 @@
package org.broadinstitute.sting.queue.engine.shell
import org.broadinstitute.sting.queue.function.CommandLineFunction
import org.broadinstitute.sting.queue.util.ShellJob
import org.broadinstitute.sting.queue.engine.{RunnerStatus, CommandLineJobRunner}
import java.util.Date
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport
import org.broadinstitute.sting.utils.Utils
import org.broadinstitute.sting.utils.runtime.{ProcessSettings, OutputStreamSettings, ProcessController}
/**
* Runs jobs one at a time locally
*/
class ShellJobRunner(val function: CommandLineFunction) extends CommandLineJobRunner {
private var runStatus: RunnerStatus.Value = _
// Controller on the thread that started the job
private var controller: ProcessController = null
/**
* Runs the function on the local shell.
* @param function Command to run.
*/
def start() {
val job = new ShellJob
val commandLine = Array("sh", jobScript.getAbsolutePath)
val stdoutSettings = new OutputStreamSettings
val stderrSettings = new OutputStreamSettings
val mergeError = (function.jobErrorFile != null)
job.workingDir = function.commandDirectory
job.outputFile = function.jobOutputFile
job.errorFile = function.jobErrorFile
stdoutSettings.setOutputFile(function.jobOutputFile, true)
if (function.jobErrorFile != null)
stderrSettings.setOutputFile(function.jobErrorFile, true)
job.shellScript = jobScript
if (logger.isDebugEnabled) {
stdoutSettings.printStandard(true)
stderrSettings.printStandard(true)
}
// Allow advanced users to update the job.
updateJobRun(job)
val processSettings = new ProcessSettings(
commandLine, mergeError, function.commandDirectory, null,
null, stdoutSettings, stderrSettings)
updateJobRun(processSettings)
getRunInfo.startTime = new Date()
getRunInfo.exechosts = Utils.resolveHostname()
updateStatus(RunnerStatus.RUNNING)
job.run()
controller = ProcessController.getThreadLocal
val exitStatus = controller.exec(processSettings).getExitValue
getRunInfo.doneTime = new Date()
updateStatus(RunnerStatus.DONE)
updateStatus(if (exitStatus == 0) RunnerStatus.DONE else RunnerStatus.FAILED)
}
override def checkUnknownStatus() {}
/**
* Possibly invoked from a shutdown thread, find and
* stop the controller from the originating thread
*/
def tryStop() {
// Assumes that after being set the job may be
// reassigned but will not be reset back to null
if (controller != null) {
try {
controller.tryDestroy()
} catch {
case e =>
logger.error("Unable to kill shell job: " + function.description)
}
}
}
}

2
public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala
View File

@ -27,7 +27,7 @@ package org.broadinstitute.sting.queue.extensions.gatk
import org.broadinstitute.sting.utils.interval.IntervalUtils
import java.io.File
import collection.JavaConversions._
import org.broadinstitute.sting.queue.util.IOUtils
import org.broadinstitute.sting.utils.io.IOUtils
import org.broadinstitute.sting.queue.function.scattergather.{CloneFunction, ScatterFunction}
import org.broadinstitute.sting.commandline.Output

2
public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/RodBind.scala
View File

@ -1,7 +1,7 @@
package org.broadinstitute.sting.queue.extensions.gatk
import java.io.File
import org.broadinstitute.sting.queue.util.FileExtension
import org.broadinstitute.sting.utils.io.FileExtension
import java.lang.String
/**

2
public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/TaggedFile.scala
View File

@ -1,7 +1,7 @@
package org.broadinstitute.sting.queue.extensions.gatk
import java.io.File
import org.broadinstitute.sting.queue.util.FileExtension
import org.broadinstitute.sting.utils.io.FileExtension
/**
* Used to provide tagged -I input_file arguments to the GATK.

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