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

This commit is contained in:
Ryan Poplin 2011-10-25 15:58:56 -04:00
parent ea5857c618 2794e5c1d4
commit 56fdf0b865
106 changed files with 3725 additions and 1361 deletions
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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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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.*;
@ -100,6 +103,8 @@ public class ParsingEngine {
if(clp != null)
argumentTypeDescriptors.addAll(clp.getArgumentTypeDescriptors());
argumentTypeDescriptors.addAll(STANDARD_ARGUMENT_TYPE_DESCRIPTORS);
addArgumentSource(ParsingEngineArgumentFiles.class);
}
/**
@ -148,21 +153,43 @@ 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 {
@ -170,10 +197,31 @@ 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,
@ -494,7 +542,7 @@ 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 );
@ -579,9 +627,21 @@ 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.");
}
@ -634,4 +694,13 @@ 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);
}
/**

31
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
View File

@ -220,12 +220,12 @@ 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;
}
/**
@ -296,10 +296,14 @@ public class GenomeAnalysisEngine {
else if(WalkerManager.getDownsamplingMethod(walker) != null)
method = WalkerManager.getDownsamplingMethod(walker);
else
method = argCollection.getDefaultDownsamplingMethod();
method = GATKArgumentCollection.getDefaultDownsamplingMethod();
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); }
@ -389,7 +393,9 @@ 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) {
@ -426,7 +432,7 @@ public class GenomeAnalysisEngine {
return new MonolithicShardStrategy(getGenomeLocParser(), readsDataSource,shardType,region);
}
ShardStrategy shardStrategy = null;
ShardStrategy shardStrategy;
ShardStrategyFactory.SHATTER_STRATEGY shardType;
long SHARD_SIZE = 100000L;
@ -435,6 +441,8 @@ 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.");
@ -498,7 +506,8 @@ 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");
}
/**
@ -729,6 +738,7 @@ 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 )
@ -757,15 +767,22 @@ 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,
@ -781,14 +798,12 @@ 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

@ -135,8 +135,8 @@ 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)
@ -146,6 +146,18 @@ 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

26
public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
View File

@ -27,7 +27,9 @@ package org.broadinstitute.sting.gatk.filters;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceRecord;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.exceptions.UserException;
/**
* Filter out malformed reads.
@ -37,14 +39,25 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
*/
public class MalformedReadFilter extends ReadFilter {
private SAMFileHeader header;
@Argument(fullName = "filter_mismatching_base_and_quals", shortName = "filterMBQ", doc = "if a read has mismatching number of bases and base qualities, filter out the read instead of blowing up.", required = false)
boolean filterMismatchingBaseAndQuals = false;
@Override
public void initialize(GenomeAnalysisEngine engine) {
this.header = engine.getSAMFileHeader();
}
public boolean filterOut(SAMRecord read) {
return !checkInvalidAlignmentStart(read) ||
// slowly changing the behavior to blow up first and filtering out if a parameter is explicitly provided
if (!checkMismatchingBasesAndQuals(read)) {
if (!filterMismatchingBaseAndQuals)
throw new UserException.MalformedBAM(read, "BAM file has a read with mismatching number of bases and base qualities. Offender: " + read.getReadName() +" [" + read.getReadLength() + " bases] [" +read.getBaseQualities().length +"] quals");
else
return true;
}
return !checkInvalidAlignmentStart(read) ||
!checkInvalidAlignmentEnd(read) ||
!checkAlignmentDisagreesWithHeader(this.header,read) ||
!checkCigarDisagreesWithAlignment(read);
@ -108,4 +121,13 @@ public class MalformedReadFilter extends ReadFilter {
return false;
return true;
}
/**
* Check if the read has the same number of bases and base qualities
* @param read the read to validate
* @return true if they have the same number. False otherwise.
*/
private static boolean checkMismatchingBasesAndQuals(SAMRecord read) {
return (read.getReadLength() == read.getBaseQualities().length);
}
}

3
public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
View File

@ -475,7 +475,8 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
}
public void onTraversalDone(ClippingData data) {
out.printf(data.toString());
if ( out != null )
out.printf(data.toString());
}
// --------------------------------------------------------------------------------------------------------------

284
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++) {
@ -410,12 +420,14 @@ public class PairHMMIndelErrorModel {
if (read == null)
continue;
if ( isReduced ) {
read = ReadUtils.reducedReadWithReducedQuals(read);
}
if(ReadUtils.is454Read(read)) {
continue;
}
double[] recalQuals = null;
// get bases of candidate haplotypes that overlap with reads
final int trailingBases = 3;
@ -534,6 +546,12 @@ 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 +569,37 @@ 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 +623,28 @@ 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];

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;
}
}

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
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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
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@ -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
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@ -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
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@ -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
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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;
}
}

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);
}
}
}
}

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/*
* 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);
}
}

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/*
* 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);
}
}

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/*
* 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();
}
}
}
}
}
}

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/*
* 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;
}
}

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/*
* 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;
}
}

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/*
* 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
}

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/*
* 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();
}

4
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
View File

@ -86,10 +86,6 @@ public class GATKSAMRecord extends SAMRecord {
if ( originalQuals != null )
mRecord.setBaseQualities(originalQuals);
}
// sanity check that the lengths of the base and quality strings are equal
if ( getBaseQualities().length != getReadLength() )
throw new UserException.MalformedBAM(this, String.format("Error: the number of base qualities does not match the number of bases in %s.", mRecord.getReadName()));
}
///////////////////////////////////////////////////////////////////////////////

4
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
View File

@ -607,7 +607,7 @@ public class VariantContextUtils {
}
// if we have more alternate alleles in the merged VC than in one or more of the
// original VCs, we need to strip out the GL/PLs (because they are no longer accurate)
// original VCs, we need to strip out the GL/PLs (because they are no longer accurate), as well as allele-dependent attributes like AC,AF
for ( VariantContext vc : VCs ) {
if (vc.alleles.size() == 1)
continue;
@ -615,6 +615,8 @@ public class VariantContextUtils {
logger.warn(String.format("Stripping PLs at %s due incompatible alleles merged=%s vs. single=%s",
genomeLocParser.createGenomeLoc(vc), alleles, vc.alleles));
genotypes = stripPLs(genotypes);
// this will remove stale AC,AF attributed from vc
calculateChromosomeCounts(vc, attributes, true);
break;
}
}

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);
}
}
}

4
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -96,8 +96,8 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
@Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "78a49597f1abf1c738e67d50c8fbed2b"); }
@Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "9253d61ddb52c429adf0e153cef494ca"); }
@Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "5012dfe65cf7e7d8f014e97e4a996aea"); }
@Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "4c63bfa5f73793aaca42e130ec49f238"); }
@Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "86e326acbd8d2af8a6040eb146d92fc6"); }
@Test public void threeWayWithRefs() {
WalkerTestSpec spec = new WalkerTestSpec(

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);
}
}

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);
}
}

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"/>

51
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
View File

@ -65,6 +65,9 @@ class DataProcessingPipeline extends QScript {
@Input(doc="Decompose input BAM file and fully realign it using BWA and assume Pair Ended reads", fullName="use_bwa_pair_ended", shortName="bwape", required=false)
var useBWApe: Boolean = false
@Input(doc="Decompose input BAM file and fully realign it using BWA SW", fullName="use_bwa_sw", shortName="bwasw", required=false)
var useBWAsw: Boolean = false
@Input(doc="Number of threads BWA should use", fullName="bwa_threads", shortName="bt", required=false)
var bwaThreads: Int = 1
@ -162,22 +165,28 @@ class DataProcessingPipeline extends QScript {
var index = 1
for (bam <- bams) {
// first revert the BAM file to the original qualities
val revertedBAM = revertBAM(bam)
val readSortedBam = swapExt(revertedBAM, ".bam", "." + index + ".sorted.bam" )
val saiFile1 = swapExt(bam, ".bam", "." + index + ".1.sai")
val saiFile2 = swapExt(bam, ".bam", "." + index + ".2.sai")
val realignedSamFile = swapExt(bam, ".bam", "." + index + ".realigned.sam")
val realignedBamFile = swapExt(bam, ".bam", "." + index + ".realigned.bam")
val rgRealignedBamFile = swapExt(bam, ".bam", "." + index + ".realigned.rg.bam")
if (useBWAse) {
val revertedBAM = revertBAM(bam, true)
add(bwa_aln_se(revertedBAM, saiFile1),
bwa_sam_se(revertedBAM, saiFile1, realignedSamFile))
}
else {
add(sortSam(revertedBAM, readSortedBam, SortOrder.queryname),
bwa_aln_pe(readSortedBam, saiFile1, 1),
bwa_aln_pe(readSortedBam, saiFile2, 2),
bwa_sam_pe(readSortedBam, saiFile1, saiFile2, realignedSamFile))
else if (useBWApe) {
val revertedBAM = revertBAM(bam, true)
add(bwa_aln_pe(revertedBAM, saiFile1, 1),
bwa_aln_pe(revertedBAM, saiFile2, 2),
bwa_sam_pe(revertedBAM, saiFile1, saiFile2, realignedSamFile))
}
else if (useBWAsw) {
val revertedBAM = revertBAM(bam, false)
val fastQ = swapExt(revertedBAM, ".bam", ".fq")
add(convertToFastQ(revertedBAM, fastQ),
bwa_sw(fastQ, realignedSamFile))
}
add(sortSam(realignedSamFile, realignedBamFile, SortOrder.coordinate))
addReadGroups(realignedBamFile, rgRealignedBamFile, new SAMFileReader(bam))
@ -196,16 +205,16 @@ class DataProcessingPipeline extends QScript {
ConsensusDeterminationModel.USE_READS
}
def revertBams(bams: List[File]): List[File] = {
def revertBams(bams: List[File], removeAlignmentInformation: Boolean): List[File] = {
var revertedBAMList: List[File] = List()
for (bam <- bams)
revertedBAMList :+= revertBAM(bam)
revertedBAMList :+= revertBAM(bam, removeAlignmentInformation)
return revertedBAMList
}
def revertBAM(bam: File): File = {
def revertBAM(bam: File, removeAlignmentInformation: Boolean): File = {
val revertedBAM = swapExt(bam, ".bam", ".reverted.bam")
add(revert(bam, revertedBAM))
add(revert(bam, revertedBAM, removeAlignmentInformation))
return revertedBAM
}
@ -226,7 +235,7 @@ class DataProcessingPipeline extends QScript {
if (nContigs < 0)
nContigs = QScriptUtils.getNumberOfContigs(bams(0))
val realignedBAMs = if (useBWApe || useBWAse) {performAlignment(bams)} else {revertBams(bams)}
val realignedBAMs = if (useBWApe || useBWAse || useBWAsw) {performAlignment(bams)} else {revertBams(bams, false)}
// generate a BAM file per sample joining all per lane files if necessary
val sampleBAMFiles: Map[String, List[File]] = createSampleFiles(bams, realignedBAMs)
@ -423,12 +432,20 @@ class DataProcessingPipeline extends QScript {
this.jobName = queueLogDir + outBam + ".rg"
}
case class revert (inBam: File, outBam: File) extends RevertSam with ExternalCommonArgs {
case class revert (inBam: File, outBam: File, removeAlignmentInfo: Boolean) extends RevertSam with ExternalCommonArgs {
this.output = outBam
this.input :+= inBam
this.removeAlignmentInformation = removeAlignmentInfo;
this.sortOrder = if (removeAlignmentInfo) {SortOrder.queryname} else {SortOrder.coordinate}
this.analysisName = queueLogDir + outBam + "revert"
this.jobName = queueLogDir + outBam + ".revert"
}
case class convertToFastQ (inBam: File, outFQ: File) extends SamToFastq with ExternalCommonArgs {
this.input :+= inBam
this.fastq = outFQ
this.analysisName = queueLogDir + outFQ + "convert_to_fastq"
this.jobName = queueLogDir + outFQ + ".convert_to_fastq"
}
case class bwa_aln_se (inBam: File, outSai: File) extends CommandLineFunction with ExternalCommonArgs {
@ -468,6 +485,14 @@ class DataProcessingPipeline extends QScript {
this.jobName = queueLogDir + outBam + ".bwa_sam_pe"
}
case class bwa_sw (inFastQ: File, outBam: File) extends CommandLineFunction with ExternalCommonArgs {
@Input(doc="fastq file to be aligned") var fq = inFastQ
@Output(doc="output bam file") var bam = outBam
def commandLine = bwaPath + " bwasw -t " + bwaThreads + " " + reference + " " + fq + " > " + bam
this.analysisName = queueLogDir + outBam + ".bwasw"
this.jobName = queueLogDir + outBam + ".bwasw"
}
case class writeList(inBams: List[File], outBamList: File) extends ListWriterFunction {
this.inputFiles = inBams
this.listFile = outBamList

13
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
View File

@ -98,13 +98,17 @@ class MethodsDevelopmentCallingPipeline extends QScript {
// BUGBUG: We no longer support b36/hg18 because several of the necessary files aren't available aligned to those references
val targetDataSets: Map[String, Target] = Map(
"NA12878_gold" -> new Target("NA12878.goldStandard", hg19, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/data/goldStandard.list"),
new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.HiSeq19.filtered.vcf"), // ** There is no gold standard for the gold standard **
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.noChrY.hg19.intervals", 2.14, 99.0, lowPass, !exome, 391),
"NA12878_wgs_b37" -> new Target("NA12878.HiSeq.WGS.b37", hg19, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.bam"),
new File("/humgen/gsa-hpprojects/dev/carneiro/hiseq19/analysis/snps/NA12878.HiSeq19.filtered.vcf"),
new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.HiSeq19.filtered.vcf"),
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.noChrY.hg19.intervals", 2.14, 99.0, !lowPass, !exome, 1),
"NA12878_wgs_decoy" -> new Target("NA12878.HiSeq.WGS.b37_decoy", b37_decoy, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37_decoy.NA12878.clean.dedup.recal.bam"),
new File("/humgen/gsa-hpprojects/dev/carneiro/hiseq19/analysis/snps/NA12878.HiSeq19.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.HiSeq19.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.noChrY.hg19.intervals", 2.14, 99.0, !lowPass, !exome, 1),
"NA12878_wgs_hg18" -> new Target("NA12878.HiSeq.WGS.hg18", hg18, dbSNP_hg18_129, hapmap_hg18,
"/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.indels.10.mask",
@ -142,7 +146,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 99.0, !lowPass, !exome, 3),
"GA2hg19" -> new Target("NA12878.GA2.hg19", hg19, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.GA2.WGS.bwa.cleaned.hg19.bam"),
new File("/humgen/gsa-hpprojects/dev/carneiro/hiseq19/analysis/snps/NA12878.GA2.hg19.filtered.vcf"),
new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.GA2.hg19.filtered.vcf"),
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.14, 99.0, !lowPass, !exome, 1),
"FIN" -> new Target("FIN", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/1kg/processing/pipeline_test_bams/FIN.79sample.Nov2010.chr20.bam"),
@ -201,7 +205,6 @@ class MethodsDevelopmentCallingPipeline extends QScript {
// 1.) Unified Genotyper Base
class GenotyperBase (t: Target) extends UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
this.memoryLimit = 3
this.reference_sequence = t.reference
this.intervalsString ++= List(t.intervals)
this.scatterCount = 140
@ -228,6 +231,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
// 1b.) Call Indels with UG
class indelCall (t: Target) extends GenotyperBase(t) {
this.memoryLimit = 6
this.out = t.rawIndelVCF
this.glm = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.INDEL
this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF
@ -255,7 +259,6 @@ class MethodsDevelopmentCallingPipeline extends QScript {
// 3.) Variant Quality Score Recalibration - Generate Recalibration table
class VQSR(t: Target, goldStandard: Boolean) extends VariantRecalibrator with UNIVERSAL_GATK_ARGS {
this.memoryLimit = 4
this.nt = 2
this.reference_sequence = t.reference
this.intervalsString ++= List(t.intervals)

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.

2
public/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala
View File

@ -50,8 +50,8 @@ trait PicardBamFunction extends JavaCommandLineFunction {
abstract override def commandLine = super.commandLine +
Array(
repeat(" INPUT=", inputBams),
" OUTPUT=" + outputBam,
" TMP_DIR=" + jobTempDir,
optional(" OUTPUT=", outputBam),
optional(" COMPRESSION_LEVEL=", compressionLevel),
optional(" VALIDATION_STRINGENCY=", validationStringency),
optional(" SO=", sortOrder),

77
public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala 100644
View File

@ -0,0 +1,77 @@
package org.broadinstitute.sting.queue.extensions.picard
import org.broadinstitute.sting.commandline._
import java.io.File
/*
* Created by IntelliJ IDEA.
* User: carneiro
* Date: 6/22/11
* Time: 10:35 AM
*/
class SamToFastq extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction {
analysisName = "SamToFastq"
javaMainClass = "net.sf.picard.sam.SamToFastq"
@Input(shortName = "input", fullName = "input_bam_files", required = true, doc = "Input SAM/BAM file to extract reads from.")
var input: List[File] = Nil
@Output(shortName = "fastq", fullName = "output_fastq_file", required = true, doc = "Output fastq file (single-end fastq or, if paired, first end of the pair fastq).")
var fastq: File = _
@Output(shortName = "se", fullName = "second_end_fastq", required = false, doc = "Output fastq file (if paired, second end of the pair fastq).")
var secondEndFastQ: File = _
@Argument(shortName = "opg", fullName = "output_per_readgroup", required = false, doc = "Output a fastq file per read group (two fastq files per read group if the group is paired).")
var outputPerReadGroup: Boolean = false
@Argument(shortName = "od", fullName = "output_dir", required = false, doc = "Directory in which to output the fastq file(s). Used only when OUTPUT_PER_RG is true.")
var outputDir: File = _
@Argument(shortName = "rr", fullName = "re_reverse", required = false, doc = "Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq.")
var reReverse: Boolean = true
@Argument(shortName = "nonpf", fullName = "include_non_pf_reads", required = false, doc = "Include non-PF reads from the SAM file into the output FASTQ files.")
var includeNonPFReads: Boolean = false
@Argument(shortName = "cat", fullName = "clipping_attribute", required = false, doc = "The attribute that stores the position at which the SAM record should be clipped.")
var clippingAttribute: String = null
@Argument(shortName = "cac", fullName = "clipping_action", required = false, doc = "The action that should be taken with clipped reads: 'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region.")
var clippingAction: String = null
@Argument(shortName = "r1t", fullName = "read_one_trim", required = false, doc = "The number of bases to trim from the beginning of read 1.")
var readOneTrim: Int = -1
@Argument(shortName = "r1mbtw", fullName = "read_one_max_bases_to_write", required = false, doc = "The maximum number of bases to write from read 1 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written.")
var readOneMaxBasesToWrite: Int = -1
@Argument(shortName = "r2t", fullName = "read_two_trim", required = false, doc = "The number of bases to trim from the beginning of read 2.")
var readTwoTrim: Int = -1
@Argument(shortName = "r2mbtw", fullName = "read_two_max_bases_to_write", required = false, doc = "The maximum number of bases to write from read 2 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written.")
var readTwoMaxBasesToWrite: Int = -1
@Argument(shortName = "inpa", fullName = "include_non_primary_alignments", required = false, doc = "If true, include non-primary alignments in the output. Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments.")
var includeNonPrimaryAlignments: Boolean = false
override def inputBams = input
override def outputBam = null
this.sortOrder = null
override def commandLine = super.commandLine +
" FASTQ=" + fastq +
optional(" SECOND_END_FASTQ=", secondEndFastQ) +
conditionalParameter(outputPerReadGroup, optional(" OUTPUT_PER_RG=", outputPerReadGroup)) +
optional(" OUTPUT_DIR=", outputDir) +
conditionalParameter(!reReverse, optional(" RE_REVERSE=", reReverse)) +
conditionalParameter(includeNonPFReads, optional(" INCLUDE_NON_PF_READS=", includeNonPFReads)) +
optional(" CLIPPING_ATTRIBUTE=", clippingAttribute) +
optional(" CLIPPING_ACTION=", clippingAction) +
conditionalParameter (readOneTrim >= 0, optional(" READ1_TRIM=", readOneTrim)) +
conditionalParameter (readOneMaxBasesToWrite >= 0, optional(" READ1_MAX_BASES_TO_WRITE=", readOneMaxBasesToWrite)) +
conditionalParameter (readTwoTrim >= 0, optional(" READ2_TRIM=", readTwoTrim)) +
conditionalParameter (readTwoMaxBasesToWrite >=0, optional(" READ2_MAX_BASES_TO_WRITE=", readTwoMaxBasesToWrite)) +
conditionalParameter (includeNonPrimaryAlignments, optional(" INCLUDE_NON_PRIMARY_ALIGNMENTS=", includeNonPrimaryAlignments))
}

2
public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala
View File

@ -25,7 +25,7 @@
package org.broadinstitute.sting.queue.function
import org.broadinstitute.sting.commandline.Argument
import org.broadinstitute.sting.queue.util.IOUtils
import org.broadinstitute.sting.utils.io.IOUtils
import java.io.File
/**

1
public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
View File

@ -31,6 +31,7 @@ import org.broadinstitute.sting.queue.{QException, QSettings}
import collection.JavaConversions._
import org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction
import org.broadinstitute.sting.queue.util._
import org.broadinstitute.sting.utils.io.IOUtils
/**
* The base interface for all functions in Queue.

5
public/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala
View File

@ -4,7 +4,8 @@ import java.io.File
import org.broadinstitute.sting.commandline.{Input, Output}
import org.broadinstitute.sting.queue.function.QFunction
import org.broadinstitute.sting.queue.QException
import org.broadinstitute.sting.queue.util.IOUtils
import org.broadinstitute.sting.utils.io.IOUtils
import collection.JavaConversions._
/**
* Base class for Gather command line functions.
@ -29,7 +30,7 @@ trait GatherFunction extends QFunction {
/**
* Waits for gather parts to propagate over NFS or throws an exception.
*/
protected def waitForGatherParts = {
protected def waitForGatherParts() {
val missing = IOUtils.waitFor(gatherParts, 120)
if (!missing.isEmpty)
throw new QException("Unable to find gather inputs: " + missing.mkString(", "))

19
public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
View File

@ -29,6 +29,7 @@ import org.broadinstitute.sting.queue.util._
import org.broadinstitute.sting.commandline.{Gatherer, Gather, ArgumentSource}
import org.broadinstitute.sting.queue.function.{QFunction, CommandLineFunction}
import org.broadinstitute.sting.queue.QException
import org.broadinstitute.sting.utils.io.IOUtils
/**
* A function that can be run faster by splitting it up into pieces and then joining together the results.
@ -82,8 +83,8 @@ trait ScatterGatherableFunction extends CommandLineFunction {
/**
* Sets the scatter gather directory to the command directory if it is not already set.
*/
override def freezeFieldValues = {
super.freezeFieldValues
override def freezeFieldValues() {
super.freezeFieldValues()
if (this.scatterGatherDirectory == null) {
if (qSettings.jobScatterGatherDirectory != null) {
@ -98,10 +99,14 @@ trait ScatterGatherableFunction extends CommandLineFunction {
* The scatter function.
*/
private lazy val scatterFunction = {
// Only depend on input fields that have a value
val inputFieldsWithValues = this.inputFields.filter(hasFieldValue(_))
val inputFiles = inputFieldsWithValues.flatMap(getFieldFiles(_)).toSet
val scatterFunction = newScatterFunction()
this.copySettingsTo(scatterFunction)
scatterFunction.originalFunction = this
scatterFunction.originalInputs = this.inputs
scatterFunction.originalInputs = inputFiles
scatterFunction.commandDirectory = this.scatterGatherTempDir("scatter")
scatterFunction.isIntermediate = true
scatterFunction.addOrder = this.addOrder :+ 1
@ -121,8 +126,6 @@ trait ScatterGatherableFunction extends CommandLineFunction {
def generateFunctions() = {
var functions = List.empty[QFunction]
// Only depend on input fields that have a value
val inputFieldsWithValues = this.inputFields.filter(hasFieldValue(_))
// Only gather up fields that will have a value
val outputFieldsWithValues = this.outputFields.filter(hasFieldValue(_))
@ -228,7 +231,7 @@ trait ScatterGatherableFunction extends CommandLineFunction {
* Calls setupScatterFunction with scatterFunction.
* @param scatterFunction The function that will create the scatter pieces in the temporary directories.
*/
protected def initScatterFunction(scatterFunction: ScatterFunction) = {
protected def initScatterFunction(scatterFunction: ScatterFunction) {
if (this.setupScatterFunction != null)
if (this.setupScatterFunction.isDefinedAt(scatterFunction))
this.setupScatterFunction(scatterFunction)
@ -272,7 +275,7 @@ trait ScatterGatherableFunction extends CommandLineFunction {
* @param gatherFunction The function that will merge the gather pieces from the temporary directories.
* @param gatherField The output field being gathered.
*/
protected def initGatherFunction(gatherFunction: GatherFunction, gatherField: ArgumentSource) = {
protected def initGatherFunction(gatherFunction: GatherFunction, gatherField: ArgumentSource) {
if (this.setupGatherFunction != null)
if (this.setupGatherFunction.isDefinedAt(gatherFunction, gatherField))
this.setupGatherFunction(gatherFunction, gatherField)
@ -289,7 +292,7 @@ trait ScatterGatherableFunction extends CommandLineFunction {
* @param cloneFunction The clone of this ScatterGatherableFunction
* @param index The one based index (from 1..scatterCount inclusive) of the scatter piece.
*/
protected def initCloneFunction(cloneFunction: CloneFunction, index: Int) = {
protected def initCloneFunction(cloneFunction: CloneFunction, index: Int) {
if (this.setupCloneFunction != null)
if (this.setupCloneFunction.isDefinedAt(cloneFunction, index))
this.setupCloneFunction(cloneFunction, index)

51
public/scala/src/org/broadinstitute/sting/queue/util/CommandLineJob.scala
View File

@ -1,51 +0,0 @@
package org.broadinstitute.sting.queue.util
import java.io.File
/**
* Base utility class for a command line job.
*/
abstract class CommandLineJob {
var shellScript: File = _
var workingDir: File = _
var inputFile: File = _
var outputFile: File = _
var errorFile: File = _
/**
* Runs the command, either immediately or dispatching it to a compute farm.
* If it is dispatched to a compute farm it should not start until jobs it depends on are finished.
*/
def run()
/**
* Returns the content of a command output.
* @param streamOutput The output of the command.
* @return The content of the command, along with a message if it was truncated.
*/
protected def content(streamOutput: ProcessController.StreamOutput) = {
var content = streamOutput.content
if (streamOutput.contentTruncated)
content += "%n%n<truncated>".format()
content
}
/**
* Returns the ProcessController for this thread.
* @return The ProcessController for this thread.
*/
protected def processController = CommandLineJob.threadProcessController.get
/** A five mb limit of characters for display. */
protected val FIVE_MB = 1024 * 512 * 5;
}
/**
* Base class for a command line job.
*/
object CommandLineJob {
/** Thread local process controller container. */
private val threadProcessController = new ThreadLocal[ProcessController] {
override def initialValue = new ProcessController
}
}

15
public/scala/src/org/broadinstitute/sting/queue/util/FileExtension.scala
View File

@ -1,15 +0,0 @@
package org.broadinstitute.sting.queue.util
import java.io.File
/**
* An trait for @Input or @Output CommandLineFunction fields that are extensions of files.
*/
trait FileExtension extends File {
/**
* Returns a clone of the FileExtension with the new path.
* @param newPath new path for the clone of this FileExtension
* @return a clone of the FileExtension with the new path.
*/
def withPath(newPath: String): File
}

253
public/scala/src/org/broadinstitute/sting/queue/util/IOUtils.scala
View File

@ -1,253 +0,0 @@
package org.broadinstitute.sting.queue.util
import org.apache.commons.io.FileUtils
import java.io.{FileReader, File}
import org.broadinstitute.sting.utils.exceptions.UserException
import org.broadinstitute.sting.queue.QException
/**
* A collection of utilities for modifying java.io.
*/
object IOUtils extends Logging {
/**
* Checks if the temp directory has been setup and throws an exception if they user hasn't set it correctly.
* @param tempDir Temporary directory.
*/
def checkTempDir(tempDir: File) {
val 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 == "/tmp") || (tempDirPath == "/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.
* @param tempDirParent Parent directory for the temp directory.
* @return The created temporary directory.
*/
def tempDir(prefix: String, suffix: String = "", tempDirParent: File) = {
if (!tempDirParent.exists && !tempDirParent.mkdirs)
throw new UserException.BadTmpDir("Could not create temp directory: " + tempDirParent)
val 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)
absolute(temp)
}
/**
* Writes content into a file.
* @param file File to write to.
* @param content Content to write.
*/
def writeContents(file: File, content: String) { FileUtils.writeStringToFile(file, content) }
/**
* Reads content of a file into a string.
* Only for use on really small files!
* @param file File to read to.
* @return content Content of the file.
*/
def readContents(file: File) = FileUtils.readFileToString(file)
/**
* 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.
*/
def writeTempFile(content: String, prefix: String, suffix: String, directory: File) = {
val tempFile = absolute(File.createTempFile(prefix, suffix, directory))
writeContents(tempFile, content)
tempFile
}
/**
* 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
*/
def waitFor(file: File, seconds: Int): Boolean = waitFor(List(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.
*/
def waitFor[T <: Traversable[File]](files: T, seconds: Int): Traversable[File] = {
var timeout = 0;
var tick = 0;
var missingFiles = files.filterNot(_.exists)
while (!missingFiles.isEmpty && timeout <= seconds) {
if (tick >= 10) {
tick = 0;
timeout += 1
}
tick += 1
try {
Thread.sleep(100)
} catch {
case ignore: InterruptedException =>
}
missingFiles = missingFiles.filterNot(_.exists)
}
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.
*/
def dirLevel(dir: File, level: Int): File = {
var directories = List.empty[File]
var parentDir = absolute(dir)
while (parentDir != null) {
directories +:= parentDir
parentDir = parentDir.getParentFile
}
if (directories.size <= level)
directories.last
else
directories(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.
*/
def absolute(parent: File, path: String): File =
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.
*/
def absolute(parent: File, file: File): File = {
val newPath =
if (file.isAbsolute)
absolutePath(file)
else
absolutePath(new File(parent, file.getPath))
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.
*/
def absolute(file: File) = {
replacePath(file, absolutePath(file))
}
private def absolutePath(file: File) = {
var fileAbs = file.getAbsoluteFile
var names = List.empty[String]
while (fileAbs != null) {
val name = fileAbs.getName
fileAbs = fileAbs.getParentFile
if (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 +:= name
}
}
names.mkString("/", "/", "")
}
private def replacePath(file: File, path: String) = {
file match {
case fileExtension: FileExtension =>
fileExtension.withPath(path)
case file: File =>
if (file.getClass != classOf[File])
throw new QException("Sub classes of java.io.File must also implement FileExtension so that the path can be modified.")
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.
*/
def tail(file: File, count: Int) = {
var tailLines = List.empty[String]
var reader = new FileReader(file)
try {
val iterator = org.apache.commons.io.IOUtils.lineIterator(reader)
var lineCount = 0
while (iterator.hasNext) {
val line = iterator.nextLine
lineCount += 1
if (lineCount > count)
tailLines = tailLines.tail
tailLines :+= line
}
} finally {
org.apache.commons.io.IOUtils.closeQuietly(reader)
}
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.
*/
def tryDelete(file: File) = {
val deleted = FileUtils.deleteQuietly(file)
if (deleted)
logger.debug("Deleted " + file)
else if (file.exists)
logger.warn("Unable to delete " + file)
deleted
}
}

11
public/scala/src/org/broadinstitute/sting/queue/util/JobExitException.scala
View File

@ -1,11 +0,0 @@
package org.broadinstitute.sting.queue.util
import org.broadinstitute.sting.queue.QException
/**
* Captures the exit code and error text from a failed process.
*/
class JobExitException(val exitText: String, val commandLine: Array[String], val exitCode: Int, val stdErr: String)
extends QException("%s%nCommand line:%n%s%nExit code: %s%nStandard error contained: %n%s"
.format(exitText, commandLine.mkString(" "), exitCode, stdErr)) {
}

369
public/scala/src/org/broadinstitute/sting/queue/util/ProcessController.scala
View File

@ -1,369 +0,0 @@
package org.broadinstitute.sting.queue.util
import java.io._
import scala.collection.mutable.{HashSet, ListMap}
/**
* 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.
*
* @author originally by Michael Koehrsen ported to scala and enhanced by Khalid Shakir
*/
class ProcessController extends Logging {
// Threads that capture stdout and stderr
private val stdoutCapture = new OutputCapture(ProcessController.STDOUT_KEY)
private val stderrCapture = new OutputCapture(ProcessController.STDERR_KEY)
// Communication channels with output capture threads
/** Holds the stdout and stderr sent to the background capture threads */
private val toCapture = new ListMap[String, ProcessController.CapturedStreamOutput]
/** Holds the results of the capture from the background capture threads.
* May be the content via toCapture or an EmptyStreamOutput if the capture was interrupted. */
private val fromCapture = new ListMap[String, ProcessController.StreamOutput]
// Start the background threads for this controller.
stdoutCapture.start()
stderrCapture.start()
/**
* 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.
*/
def exec(settings: ProcessController.ProcessSettings): ProcessController.ProcessOutput = {
var builder = new ProcessBuilder(settings.cmdarray:_*)
builder.directory(settings.directory)
if (settings.environment != null) {
val builderEnvironment = builder.environment
builderEnvironment.clear()
settings.environment.foreach{case (name, value) => builderEnvironment.put(name, value)}
}
builder.redirectErrorStream(settings.redirectErrorStream)
var stdout: ProcessController.StreamOutput = null
var stderr: ProcessController.StreamOutput = null
val process = builder.start
ProcessController.running.add(process)
try {
val stdoutSettings = if (settings.stdoutSettings == null) ProcessController.EmptyStreamSettings else settings.stdoutSettings
val stderrSettings = if (settings.stderrSettings == null) ProcessController.EmptyStreamSettings else settings.stderrSettings
toCapture.synchronized {
toCapture.put(ProcessController.STDOUT_KEY, new ProcessController.CapturedStreamOutput(process.getInputStream, stdoutSettings, scala.Console.out))
toCapture.put(ProcessController.STDERR_KEY, new ProcessController.CapturedStreamOutput(process.getErrorStream, stderrSettings, scala.Console.err))
toCapture.notifyAll()
}
if (settings.stdinSettings.input != null) {
val writer = new OutputStreamWriter(process.getOutputStream)
writer.write(settings.stdinSettings.input)
writer.flush()
}
if (settings.stdinSettings.inputFile != null) {
val reader = new FileReader(settings.stdinSettings.inputFile)
val writer = new OutputStreamWriter(process.getOutputStream)
val buf = new Array[Char](4096)
var readCount = 0
while ({readCount = reader.read(buf); readCount} >= 0)
writer.write(buf, 0, readCount)
writer.flush()
reader.close()
}
try {
process.getOutputStream.close()
process.waitFor()
} finally {
while (stdout == null || stderr == null) {
fromCapture.synchronized {
fromCapture.remove(ProcessController.STDOUT_KEY) match {
case Some(stream) => stdout = stream
case None => /* ignore */
}
fromCapture.remove(ProcessController.STDERR_KEY) match {
case Some(stream) => stderr = stream
case None => /* ignore */
}
try {
if (stdout == null || stderr == null)
fromCapture.wait()
} catch {
case e: InterruptedException =>
logger.error(e)
}
}
}
}
} finally {
ProcessController.running.remove(process)
}
new ProcessController.ProcessOutput(process.exitValue, stdout, stderr)
}
/** Ensures that the threads used to manipulate the IO for the process are cleaned up properly. */
def close() = {
try {
stdoutCapture.interrupt()
stderrCapture.interrupt()
} catch {
case e =>
logger.error(e)
}
}
/** calls close() */
override def finalize = close()
/**
* 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.
*/
private class OutputCapture(private val key: String)
extends Thread("OutputCapture-" + key + "-" + Thread.currentThread.getName) {
setDaemon(true)
/** Runs the capture. */
override def run = {
var break = false
while (!break) {
var processStream: ProcessController.StreamOutput = ProcessController.EmptyStreamOutput
try {
// Wait for a new input stream to be passed from this process controller.
var capturedProcessStream: ProcessController.CapturedStreamOutput = null
while (capturedProcessStream == null) {
toCapture.synchronized {
toCapture.remove(key) match {
case Some(stream) => capturedProcessStream = stream
case None => toCapture.wait()
}
}
}
// Read in the input stream
processStream = capturedProcessStream
capturedProcessStream.read
} catch {
case e: InterruptedException => {
logger.info("OutputReader interrupted, exiting")
break = true
}
case e: IOException => {
logger.error("Error reading process output", e)
}
} finally {
// Send the string back to the process controller.
fromCapture.synchronized {
fromCapture.put(key, processStream)
fromCapture.notify()
}
}
}
}
}
}
/**
* 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.
*
* @author originally by Michael Koehrsen ported to scala and enhanced by Khalid Shakir
*/
object ProcessController extends Logging {
/**
* Settings that define how to run a process.
* @param cmdarray Command line to run.
* @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.
* @param redirectErrorStream true if stderr should be sent to stdout.
*/
class ProcessSettings(val cmdarray: Array[String], val environment: Map[String, String], val directory: File,
val stdinSettings: InputStreamSettings, val stdoutSettings: OutputStreamSettings,
val stderrSettings: OutputStreamSettings, val redirectErrorStream: Boolean)
/**
* Settings that define text to write to the process stdin.
* @param input String to write to stdin.
* @param inputFile File to write to stdin.
*/
class InputStreamSettings(val input: String, val inputFile: File)
/**
* Settings that define text to capture from a process stream.
* @param stringSize The number of characters to capture, or -1 for unlimited.
* @param outputFile The file to write output to, or null to skip output.
* @param outputFileAppend true if the output file should be appended to.
*/
class OutputStreamSettings(val stringSize: Int, val outputFile: File, val outputFileAppend: Boolean)
/**
* 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.
*/
class ProcessOutput(val exitValue: Int, val stdout: StreamOutput, val stderr: StreamOutput)
/**
* The base class of stream output.
*/
abstract class StreamOutput {
/**
* Returns the content as a string.
* @return The content as a string.
*/
def content: String
/**
* Returns true if the content was truncated.
* @return true if the content was truncated.
*/
def contentTruncated: Boolean
}
private var currentCaptureId = 0
/**
* Returns the next output capture id.
* @return The next output capture id.
*/
private def NEXT_OUTPUT_CAPTURE_ID = {
currentCaptureId += 1
currentCaptureId
}
private val STDOUT_KEY = "stdout"
private val STDERR_KEY = "stderr"
/** Tracks running processes so that they can be killed as the JVM shuts down. */
private val running = new HashSet[Process]
def shutdown() = {
for (process <- running.clone) {
logger.warn("Killing: " + process)
try {
process.destroy
} catch {
case _ => /* ignore */
}
}
}
/** Empty stream settings used when no output is requested. */
private object EmptyStreamSettings extends OutputStreamSettings(0, null, false)
/** Empty stream output when no output is captured due to an error. */
private object EmptyStreamOutput extends StreamOutput {
def content = ""
def contentTruncated = false
}
/**
* Stream output captured from a stream.
* @param stream Stream to capture output.
* @param settings Settings that define what to capture.
*/
private class CapturedStreamOutput(val stream: InputStream, val settings: OutputStreamSettings, val debugStream: PrintStream) extends StreamOutput {
/**
* Returns the captured content as a string.
* @return The captured content as a string.
*/
def content = stringWriter.toString()
/**
* Returns true if the captured content was truncated.
* @return true if the captured content was truncated.
*/
def contentTruncated = stringTruncated
/**
* Drain the input stream to keep the process from backing up until it's empty.
*/
def read() = {
val reader = new InputStreamReader(stream)
val buf = new Array[Char](4096)
var readCount = 0
while ({readCount = reader.read(buf); readCount} >= 0) {
writeString(buf, readCount)
writeFile(buf, readCount)
}
closeFile()
stream.close()
}
/** The string to write capture content. */
private lazy val stringWriter = if (settings.stringSize < 0) new StringWriter else new StringWriter(settings.stringSize)
/** True if the content is truncated. */
private var stringTruncated = false
/** The number of characters left until the buffer is full. */
private var stringRemaining = settings.stringSize
/**
* Writes the buffer to the stringWriter up to stringRemaining characters.
* @param chars Character buffer to write.
* @param len Number of characters in the buffer.
*/
private def writeString(chars: Array[Char], len: Int) = {
// If debug is enabled bypass the logger and dump directly to the screen
if (logger.isDebugEnabled)
debugStream.print(new String(chars, 0, len))
if (settings.stringSize < 0) {
stringWriter.write(chars, 0, len)
} else {
if (!stringTruncated) {
stringWriter.write(chars, 0, if (len > stringRemaining) stringRemaining else len)
stringRemaining -= len
if (stringRemaining < 0)
stringTruncated = true
}
}
}
/** The file writer to capture content or null if no output file was requested. */
private lazy val fileWriter = {
if (settings.outputFile == null) {
null
} else {
new FileWriter(settings.outputFile, settings.outputFileAppend)
}
}
/**
* Writes the buffer to the fileWriter if it is not null.
* @param chars Character buffer to write.
* @param len Number of characters in the buffer.
*/
private def writeFile(chars: Array[Char], len: Int) = {
if (fileWriter != null) {
fileWriter.write(chars, 0, len)
fileWriter.flush()
}
}
/** Closes the fileWriter if it is not null. */
private def closeFile() = {
if (fileWriter != null) {
fileWriter.flush
fileWriter.close
}
}
}
}

14
public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala
View File

@ -23,15 +23,15 @@
*/
package org.broadinstitute.sting.queue.util
import org.broadinstitute.sting.queue.function.QFunction
import org.broadinstitute.sting.gatk.report.{GATKReportTable, GATKReport}
import org.broadinstitute.sting.utils.exceptions.UserException
import org.broadinstitute.sting.queue.engine.JobRunInfo
import java.io.{FileOutputStream, PrintStream, File}
import org.broadinstitute.sting.queue.function.scattergather.{GathererFunction, ScatterFunction}
import org.broadinstitute.sting.utils.R.RScriptExecutor.RScriptArgumentCollection
import org.broadinstitute.sting.utils.R.RScriptExecutor
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.utils.R.{RScriptLibrary, RScriptExecutor}
import org.broadinstitute.sting.utils.io.Resource
/**
* A mixin to add Job info to the class
@ -104,10 +104,12 @@ object QJobReport {
stream.close()
}
def plotReport(args: RScriptArgumentCollection, jobReportFile: File) {
def plotReport(args: RScriptArgumentCollection, reportFile: File, pdfFile: File) {
val executor = new RScriptExecutor(args, false) // don't except on error
val pdf = jobReportFile.getAbsolutePath + ".pdf"
executor.callRScripts(JOB_REPORT_QUEUE_SCRIPT, jobReportFile.getAbsolutePath, pdf)
executor.addLibrary(RScriptLibrary.GSALIB)
executor.addScript(new Resource(JOB_REPORT_QUEUE_SCRIPT, classOf[QJobReport]))
executor.addArgs(reportFile.getAbsolutePath, pdfFile.getAbsolutePath)
executor.exec()
}
def workAroundSameJobNames(func: QFunction):String = {

27
public/scala/src/org/broadinstitute/sting/queue/util/ShellJob.scala
View File

@ -1,27 +0,0 @@
package org.broadinstitute.sting.queue.util
/**
* Runs a job on the command line by invoking "sh -c <command>"
*/
class ShellJob extends CommandLineJob with Logging {
/**
* Runs the command and waits for the output.
*/
def run() = {
val (redirectError, errorFile) = if (this.errorFile == null) (true, null) else (false, this.errorFile)
val bufferSize = if (redirectError || logger.isDebugEnabled) FIVE_MB else 0
val stdinSettings = new ProcessController.InputStreamSettings(null, this.inputFile)
val stdoutSettings = new ProcessController.OutputStreamSettings(bufferSize, this.outputFile, true)
val stderrSettings = new ProcessController.OutputStreamSettings(FIVE_MB, errorFile, true)
val commandLine = Array("sh", shellScript.toString)
val processSettings = new ProcessController.ProcessSettings(
commandLine, null, this.workingDir, stdinSettings, stdoutSettings, stderrSettings, redirectError)
val output = processController.exec(processSettings)
if (output.exitValue != 0) {
val streamOutput = if (redirectError) output.stdout else output.stderr
throw new JobExitException("Failed to run job.", commandLine, output.exitValue, content(streamOutput))
}
}
}

7
public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
View File

@ -33,7 +33,7 @@ import java.text.SimpleDateFormat
import org.broadinstitute.sting.BaseTest
import org.broadinstitute.sting.MD5DB
import org.broadinstitute.sting.queue.QCommandLine
import org.broadinstitute.sting.queue.util.{Logging, ProcessController}
import org.broadinstitute.sting.queue.util.Logging
import java.io.File
import org.broadinstitute.sting.gatk.report.GATKReport
import org.apache.commons.io.FileUtils
@ -217,11 +217,6 @@ object PipelineTest extends BaseTest with Logging {
Runtime.getRuntime.addShutdownHook(new Thread {
/** Cleanup as the JVM shuts down. */
override def run() {
try {
ProcessController.shutdown()
} catch {
case _ => /*ignore */
}
runningCommandLines.foreach(commandLine =>
try {
commandLine.shutdown()

122
public/scala/test/org/broadinstitute/sting/queue/util/IOUtilsUnitTest.scala
View File

@ -1,122 +0,0 @@
package org.broadinstitute.sting.queue.util
import org.broadinstitute.sting.BaseTest
import java.io.File
import org.broadinstitute.sting.utils.exceptions.UserException
import org.testng.Assert
import org.testng.annotations.Test
class IOUtilsUnitTest extends BaseTest {
@Test
def testGoodTempDir = {
IOUtils.checkTempDir(new File("/tmp/queue"))
}
@Test(expectedExceptions=Array(classOf[UserException.BadTmpDir]))
def testBadTempDir = {
IOUtils.checkTempDir(new File("/tmp"))
}
@Test
def testAbsoluteSubDir = {
var 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
def testRelativeSubDir = {
var 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
def testDottedSubDir = {
var 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
def testTempDir = {
val tempDir = IOUtils.tempDir("Q-Unit-Test", "", new File("queueTempDirToDelete"))
Assert.assertTrue(tempDir.exists)
Assert.assertFalse(tempDir.isFile)
Assert.assertTrue(tempDir.isDirectory)
val deleted = IOUtils.tryDelete(tempDir)
Assert.assertTrue(deleted)
Assert.assertFalse(tempDir.exists)
}
@Test
def testDirLevel = {
var 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
def testAbsolute = {
var 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
def testTail = {
val lines = List(
"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")
val tail = IOUtils.tail(new File(BaseTest.hg18Reference + ".fai"), 5)
Assert.assertEquals(tail.size, 5)
for (i <- 0 until 5)
Assert.assertEquals(tail(i), lines(i))
}
}

73
public/scala/test/org/broadinstitute/sting/queue/util/ShellJobUnitTest.scala
View File

@ -1,73 +0,0 @@
package org.broadinstitute.sting.queue.util
import org.broadinstitute.sting.BaseTest
import org.testng.annotations.Test
import org.testng.Assert
class ShellJobUnitTest {
@Test
def testEcho {
val job = new ShellJob
job.shellScript = writeScript("echo Hello World")
job.run()
}
@Test(expectedExceptions=Array(classOf[JobExitException]))
def testBadQuotes {
val job = new ShellJob
job.shellScript = writeScript("echo 'Hello World")
job.run()
}
@Test
def testGoodQuotes {
val job = new ShellJob
job.shellScript = writeScript("echo 'Hello World'")
job.run()
}
@Test
def testEscapeCharacters {
var job: ShellJob = null
job = new ShellJob
job.shellScript = writeScript("echo #")
job.outputFile = BaseTest.createTempFile("temp", "")
job.run()
Assert.assertEquals(IOUtils.readContents(job.outputFile).trim, "")
job = new ShellJob
job.shellScript = writeScript("""echo \#""")
job.outputFile = BaseTest.createTempFile("temp", "")
job.run()
Assert.assertEquals(IOUtils.readContents(job.outputFile).trim, "#")
job = new ShellJob
job.shellScript = writeScript("""echo \\#""")
job.outputFile = BaseTest.createTempFile("temp", "")
job.run()
Assert.assertEquals(IOUtils.readContents(job.outputFile).trim, """\#""")
}
@Test
def testLongCommand {
// 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>
val builder = new StringBuilder
builder.append("echo ")
for (i <- 1 to 500) {
val s = i.toString
builder.append("000".take(3-s.length)).append(s).append("______ ")
}
val job = new ShellJob
job.shellScript = writeScript(builder.toString)
job.run()
}
private def writeScript(contents: String) = {
val file = BaseTest.createTempFile("temp", "")
IOUtils.writeContents(file, contents)
file
}
}

BIN
settings/repository/edu.mit.broad/picard-private-parts-2034.jar
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BIN
settings/repository/edu.mit.broad/picard-private-parts-2068.jar 100644
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2
settings/repository/edu.mit.broad/picard-private-parts-2034.xml → settings/repository/edu.mit.broad/picard-private-parts-2068.xml
View File

@ -1,3 +1,3 @@
<ivy-module version="1.0">
<info organisation="edu.mit.broad" module="picard-private-parts" revision="2034" status="integration" publication="20110718185300" />
<info organisation="edu.mit.broad" module="picard-private-parts" revision="2068" status="integration" publication="20111024162900" />
</ivy-module>

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