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

This commit is contained in:
Mauricio Carneiro 2011-10-18 15:23:05 -04:00
parent e12ffb6547 2125c4f38f
commit c27e2fb676
13 changed files with 281 additions and 95 deletions
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158
build.xml
View File

@ -67,6 +67,8 @@
<!-- If running the 'package' task, this property controls the name of the xml file to package --> <!-- If running the 'package' task, this property controls the name of the xml file to package -->
<property name="package.xml.dir" value="${public.dir}/packages" /> <property name="package.xml.dir" value="${public.dir}/packages" />
<property name="package.output.dir" value="${dist.dir}/packages" />
<property name="staging.dir" value="staging" />
<property name="executable" value="GenomeAnalysisTK" /> <property name="executable" value="GenomeAnalysisTK" />
<property environment="env"/> <property environment="env"/>
@ -118,6 +120,16 @@
</fileset> </fileset>
</path> </path>
<path id="testng.dependencies">
<fileset dir="${lib.dir}">
<include name="jcommander*.jar"/>
<include name="guice*.jar"/>
<include name="junit*.jar"/>
<include name="bsh*.jar"/>
<include name="snakeyaml*.jar"/>
</fileset>
</path>
<path id="build.results"> <path id="build.results">
<fileset dir="dist"> <fileset dir="dist">
<patternset refid="dependency.mask" /> <patternset refid="dependency.mask" />
@ -509,7 +521,7 @@
docletpathref="doclet.classpath" docletpathref="doclet.classpath"
classpathref="external.dependencies" classpathref="external.dependencies"
classpath="${java.classes}" classpath="${java.classes}"
additionalparam="${gatkdocs.include.hidden.arg} -private -build-timestamp &quot;${build.timestamp}&quot; -absolute-version ${build.version} -quiet -J-Xdebug -J-Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=5005"> <!-- -test to only do DocumentationTest walker --> additionalparam="${gatkdocs.include.hidden.arg} -private -build-timestamp &quot;${build.timestamp}&quot; -absolute-version ${build.version} -quiet"> <!-- -test to only do DocumentationTest walker -->
<sourcefiles> <sourcefiles>
<union> <union>
<fileset refid="all.java.source.files"/> <fileset refid="all.java.source.files"/>
@ -829,10 +841,54 @@
<target name="test.compile" depends="init.usecontracts,test.java.compile,test.scala.compile" /> <target name="test.compile" depends="init.usecontracts,test.java.compile,test.scala.compile" />
<path id="testng.default.classpath">
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />
<pathelement location="${scala.classes}" />
<pathelement location="${java.contracts}" />
<pathelement location="${java.public.test.classes}" />
<pathelement location="${java.private.test.classes}" />
<pathelement location="${scala.public.test.classes}" />
<pathelement location="${scala.private.test.classes}" />
</path>
<path id="testng.gatk.releasetest.classpath">
<path refid="testng.dependencies" />
<path>
<fileset dir="${package.output.dir}">
<include name="**/${executable}.jar" />
</fileset>
</path>
<pathelement location="${java.contracts}" />
<pathelement location="${java.public.test.classes}" />
<pathelement location="${scala.public.test.classes}" />
<pathelement location="${scala.classes}" />
<path>
<fileset dir="${lib.dir}">
<include name="scala*.jar"/>
<include name="jna*.jar"/>
</fileset>
</path>
</path>
<path id="testng.queue.releasetest.classpath">
<path refid="testng.dependencies" />
<path>
<fileset dir="${package.output.dir}">
<include name="**/${executable}.jar" />
</fileset>
</path>
<pathelement location="${java.contracts}" />
<pathelement location="${java.public.test.classes}" />
<pathelement location="${scala.public.test.classes}" />
</path>
<!-- TEST --> <!-- TEST -->
<macrodef name="run-test"> <macrodef name="run-test">
<attribute name="testtype"/> <attribute name="testtype"/>
<attribute name="outputdir"/> <attribute name="outputdir"/>
<attribute name="classpath"/>
<attribute name="runfailed"/> <attribute name="runfailed"/>
<sequential> <sequential>
@ -853,6 +909,7 @@
<echo message="Sting: Running @{testtype} test cases!"/> <echo message="Sting: Running @{testtype} test cases!"/>
<taskdef resource="testngtasks" classpath="${testng.jar}"/> <taskdef resource="testngtasks" classpath="${testng.jar}"/>
<testng outputDir="@{outputdir}" <testng outputDir="@{outputdir}"
classpathref="@{classpath}"
haltOnFailure="false" failureProperty="test.failure" haltOnFailure="false" failureProperty="test.failure"
verbose="2" verbose="2"
workingDir="${basedir}" workingDir="${basedir}"
@ -865,16 +922,6 @@
<jvmarg line="${cofoja.jvm.args}"/> <jvmarg line="${cofoja.jvm.args}"/>
<!-- <jvmarg value="-Xdebug"/> --> <!-- <jvmarg value="-Xdebug"/> -->
<!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> --> <!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
<classpath>
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />
<pathelement location="${scala.classes}" />
<pathelement location="${java.contracts}" />
<pathelement location="${java.public.test.classes}" />
<pathelement location="${java.private.test.classes}" />
<pathelement location="${scala.public.test.classes}" />
<pathelement location="${scala.private.test.classes}" />
</classpath>
<classfileset dir="${java.public.test.classes}" includes="**/@{testtype}.class"/> <classfileset dir="${java.public.test.classes}" includes="**/@{testtype}.class"/>
<classfileset dir="${java.private.test.classes}" erroronmissingdir="false"> <classfileset dir="${java.private.test.classes}" erroronmissingdir="false">
@ -904,6 +951,10 @@
</sequential> </sequential>
</macrodef> </macrodef>
<target name="test.init">
<property name="testng.classpath" value="testng.default.classpath" />
</target>
<target name="alltests"> <target name="alltests">
<antcall target="test" inheritAll="false"/> <antcall target="test" inheritAll="false"/>
<antcall target="integrationtest" inheritAll="false"/> <antcall target="integrationtest" inheritAll="false"/>
@ -916,62 +967,81 @@
<antcall target="pipelinetest.public" inheritAll="false"/> <antcall target="pipelinetest.public" inheritAll="false"/>
</target> </target>
<target name="alltests.gatk.packagejar" depends="init.buildpublic,package">
<antcall target="test.public" inheritAll="false">
<param name="testng.classpath" value="testng.gatk.releasetest.classpath" />
</antcall>
<antcall target="integrationtest.public" inheritAll="false">
<param name="testng.classpath" value="testng.gatk.releasetest.classpath" />
</antcall>
</target>
<target name="alltests.queue.packagejar" depends="init.buildpublic,queue">
<antcall target="package" inheritAll="false">
<param name="executable" value="Queue" />
</antcall>
<antcall target="pipelinetest.public" inheritAll="false">
<param name="executable" value="Queue" />
<param name="testng.classpath" value="testng.queue.releasetest.classpath" />
</antcall>
</target>
<!-- Our four different test conditions: Test, IntegrationTest, PerformanceTest, PipelineTest --> <!-- Our four different test conditions: Test, IntegrationTest, PerformanceTest, PipelineTest -->
<target name="test" depends="init.buildall,test.compile,vcf.jar" description="Run unit tests"> <target name="test" depends="init.buildall,test.compile,vcf.jar,test.init" description="Run unit tests">
<condition property="ttype" value="*UnitTest" else="${single}"> <condition property="ttype" value="*UnitTest" else="${single}">
<not><isset property="single"/></not> <not><isset property="single"/></not>
</condition> </condition>
<run-test testtype="${ttype}" outputdir="${report}/${ttype}" runfailed="false"/> <run-test testtype="${ttype}" outputdir="${report}/${ttype}" classpath="${testng.classpath}" runfailed="false"/>
</target> </target>
<target name="test.public" depends="init.buildpublic,test"/> <target name="test.public" depends="init.buildpublic,test"/>
<target name="integrationtest" depends="init.buildall,test.compile" description="Run integration tests"> <target name="integrationtest" depends="init.buildall,test.compile,test.init" description="Run integration tests">
<condition property="itype" value="*IntegrationTest" else="${single}"> <condition property="itype" value="*IntegrationTest" else="${single}">
<not><isset property="single"/></not> <not><isset property="single"/></not>
</condition> </condition>
<run-test testtype="${itype}" outputdir="${report}/${itype}" runfailed="false"/> <run-test testtype="${itype}" outputdir="${report}/${itype}" classpath="${testng.classpath}" runfailed="false"/>
</target> </target>
<target name="integrationtest.public" depends="init.buildpublic,integrationtest"/> <target name="integrationtest.public" depends="init.buildpublic,integrationtest"/>
<target name="performancetest" depends="init.buildall,test.compile" description="Run performance tests"> <target name="performancetest" depends="init.buildall,test.compile,test.init" description="Run performance tests">
<condition property="ptype" value="*PerformanceTest" else="${single}"> <condition property="ptype" value="*PerformanceTest" else="${single}">
<not><isset property="single"/></not> <not><isset property="single"/></not>
</condition> </condition>
<run-test testtype="${ptype}" outputdir="${report}/${ptype}" runfailed="false"/> <run-test testtype="${ptype}" outputdir="${report}/${ptype}" classpath="${testng.classpath}" runfailed="false"/>
</target> </target>
<target name="performancetest.public" depends="init.buildpublic,performancetest" /> <target name="performancetest.public" depends="init.buildpublic,performancetest" />
<target name="pipelinetest" depends="init.buildall,test.compile" description="Run pipeline tests"> <target name="pipelinetest" depends="init.buildall,test.compile,test.init" description="Run pipeline tests">
<condition property="pipetype" value="*PipelineTest" else="${single}"> <condition property="pipetype" value="*PipelineTest" else="${single}">
<not><isset property="single"/></not> <not><isset property="single"/></not>
</condition> </condition>
<run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" runfailed="false"/> <run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" classpath="${testng.classpath}" runfailed="false"/>
</target> </target>
<target name="pipelinetest.public" depends="init.buildpublic,pipelinetest" /> <target name="pipelinetest.public" depends="init.buildpublic,pipelinetest" />
<target name="pipelinetestrun" depends="init.buildall,test.compile" description="Run pipeline tests"> <target name="pipelinetestrun" depends="init.buildall,test.compile,test.init" description="Run pipeline tests">
<property name="pipeline.run" value="run"/> <property name="pipeline.run" value="run"/>
<condition property="pipetype" value="*PipelineTest" else="${single}"> <condition property="pipetype" value="*PipelineTest" else="${single}">
<not><isset property="single"/></not> <not><isset property="single"/></not>
</condition> </condition>
<run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" runfailed="false"/> <run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" classpath="${testng.classpath}" runfailed="false"/>
</target> </target>
<target name="pipelinetestrun.public" depends="init.buildpublic,pipelinetestrun" /> <target name="pipelinetestrun.public" depends="init.buildpublic,pipelinetestrun" />
<target name="failed-test" depends="init.buildall,test.compile"> <target name="failed-test" depends="init.buildall,test.compile,test.init">
<run-test testtype="${report}/*UnitTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/> <run-test testtype="${report}/*UnitTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" runfailed="true"/>
</target> </target>
<target name="failed-integration" depends="init.buildall,test.compile"> <target name="failed-integration" depends="init.buildall,test.compile,test.init">
<run-test testtype="${report}/*IntegrationTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/> <run-test testtype="${report}/*IntegrationTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" runfailed="true"/>
</target> </target>
<target name="failed-performance" depends="init.buildall,test.compile"> <target name="failed-performance" depends="init.buildall,test.compile,test.init">
<run-test testtype="${report}/*PerformanceTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/> <run-test testtype="${report}/*PerformanceTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" runfailed="true"/>
</target> </target>
<target name="failed-pipeline" depends="init.buildall,test.compile"> <target name="failed-pipeline" depends="init.buildall,test.compile,test.init">
<run-test testtype="${report}/*PipelineTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/> <run-test testtype="${report}/*PipelineTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" runfailed="true"/>
</target> </target>
<!-- ******************************************************************************** --> <!-- ******************************************************************************** -->
@ -1029,14 +1099,14 @@
<!-- Unzip all classes from their current locations and assemble them in a staging directory --> <!-- Unzip all classes from their current locations and assemble them in a staging directory -->
<target name="stage" description="stage files for distribution"> <target name="stage" description="stage files for distribution">
<mkdir dir="staging"/> <mkdir dir="${staging.dir}"/>
<!-- <!--
HACK: Create the edu directory before EDU on case-insensitive mac filesystems. HACK: Create the edu directory before EDU on case-insensitive mac filesystems.
The ivy dependency colt -> concurrent contains an EDU.oswego package which The ivy dependency colt -> concurrent contains an EDU.oswego package which
BCEL doesn't even pull in but messes up edu.mit.broad. BCEL doesn't even pull in but messes up edu.mit.broad.
--> -->
<mkdir dir="staging/edu"/> <mkdir dir="${staging.dir}/edu"/>
<unjar dest="staging" overwrite="false"> <unjar dest="${staging.dir}" overwrite="false">
<fileset dir="${dist.dir}"> <fileset dir="${dist.dir}">
<patternset refid="dependency.mask" /> <patternset refid="dependency.mask" />
</fileset> </fileset>
@ -1045,8 +1115,8 @@
<!-- Build a package consisting of all supporting files --> <!-- Build a package consisting of all supporting files -->
<target name="package" depends="dist,stage" description="bundle up an executable for distribution"> <target name="package" depends="dist,stage" description="bundle up an executable for distribution">
<mkdir dir="dist/packages" /> <mkdir dir="${package.output.dir}" />
<xslt destdir="dist/packages" style="${package.xml.dir}/CreatePackager.xsl" useImplicitFileset="false"> <xslt destdir="${package.output.dir}" style="${package.xml.dir}/CreatePackager.xsl" useImplicitFileset="false">
<flattenmapper/> <flattenmapper/>
<fileset dir="${package.xml.dir}"> <fileset dir="${package.xml.dir}">
<include name="${executable}.xml" /> <include name="${executable}.xml" />
@ -1057,11 +1127,11 @@
</fileset> </fileset>
</xslt> </xslt>
<ant antfile="${dist.dir}/packages/${executable}.xml" target="package" /> <ant antfile="${package.output.dir}/${executable}.xml" target="package" />
</target> </target>
<target name="release" depends="package" description="release a build, putting each file in a location specified by the package"> <target name="release" depends="package" description="release a build, putting each file in a location specified by the package">
<ant antfile="${dist.dir}/packages/${executable}.xml" target="release" /> <ant antfile="${package.output.dir}/${executable}.xml" target="release" />
</target> </target>
<!-- Build a subset of picard with only those classes we need by completely abusing the packaging system --> <!-- Build a subset of picard with only those classes we need by completely abusing the packaging system -->
@ -1070,7 +1140,7 @@
<!-- Build out a classpath --> <!-- Build out a classpath -->
<pathconvert property="required.picard.jars" pathsep=":"> <pathconvert property="required.picard.jars" pathsep=":">
<fileset dir="${basedir}"> <fileset dir="${basedir}">
<include name="staging" /> <include name="${staging.dir}" />
<include name="${lib.dir}/picard-*.*.*.jar" /> <include name="${lib.dir}/picard-*.*.*.jar" />
<include name="${lib.dir}/sam-*.jar" /> <include name="${lib.dir}/sam-*.jar" />
</fileset> </fileset>
@ -1078,14 +1148,14 @@
<echo message="required.picard.jars=${required.picard.jars}" /> <echo message="required.picard.jars=${required.picard.jars}" />
<!-- Stage picard-private --> <!-- Stage picard-private -->
<delete dir="staging" /> <delete dir="${staging.dir}" />
<mkdir dir="staging" /> <mkdir dir="${staging.dir}" />
<unjar src="${picard.dist.dir}/picard-private.jar" dest="staging" overwrite="true" /> <unjar src="${picard.dist.dir}/picard-private.jar" dest="${staging.dir}" overwrite="true" />
<!-- Use the packaging system to extract parts of picard-private we need --> <!-- Use the packaging system to extract parts of picard-private we need -->
<mkdir dir="${dist.dir}/packages" /> <mkdir dir="${package.output.dir}" />
<xslt in="${package.xml.dir}/PicardPrivate.xml" out="${dist.dir}/packages/BuildPicardPrivate.xml" style="${package.xml.dir}/CreatePackager.xsl" /> <xslt in="${package.xml.dir}/PicardPrivate.xml" out="${package.output.dir}/BuildPicardPrivate.xml" style="${package.xml.dir}/CreatePackager.xsl" />
<ant antfile="${dist.dir}/packages/BuildPicardPrivate.xml"> <ant antfile="${package.output.dir}/BuildPicardPrivate.xml">
<property name="additional.jars" value="${required.picard.jars}" /> <property name="additional.jars" value="${required.picard.jars}" />
</ant> </ant>
</target> </target>
@ -1121,7 +1191,7 @@
<delete dir="${build.dir}"/> <delete dir="${build.dir}"/>
<delete dir="${lib.dir}"/> <delete dir="${lib.dir}"/>
<delete dir="dump"/> <delete dir="dump"/>
<delete dir="staging"/> <delete dir="${staging.dir}"/>
<delete dir="${dist.dir}"/> <delete dir="${dist.dir}"/>
<delete dir="pipelinetests"/> <delete dir="pipelinetests"/>
</target> </target>

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

@ -379,8 +379,10 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
} }
if ( tribbleType == null ) if ( tribbleType == null )
if ( ! file.canRead() | ! file.isFile() ) { if ( ! file.exists() ) {
throw new UserException.BadArgumentValue(name, "Couldn't read file to determine type: " + file); throw new UserException.CouldNotReadInputFile(file, "file does not exist");
} else if ( ! file.canRead() || ! file.isFile() ) {
throw new UserException.CouldNotReadInputFile(file, "file could not be read");
} else { } else {
throw new UserException.CommandLineException( throw new UserException.CommandLineException(
String.format("No tribble type was provided on the command line and the type of the file could not be determined dynamically. " + String.format("No tribble type was provided on the command line and the type of the file could not be determined dynamically. " +

13
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -133,7 +134,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
/** /**
* By default, this tool throws a UserException when it encounters a field without a value in some record. This * By default, this tool throws a UserException when it encounters a field without a value in some record. This
* is generally useful when you mistype -F CHROM, so that you get a friendly warning about CHRMO not being * is generally useful when you mistype -F CHROM, so that you get a friendly warning about CHROM not being
* found before the tool runs through 40M 1000G records. However, in some cases you genuinely want to allow such * found before the tool runs through 40M 1000G records. However, in some cases you genuinely want to allow such
* fields (e.g., AC not being calculated for filtered records, if included). When provided, this argument * fields (e.g., AC not being calculated for filtered records, if included). When provided, this argument
* will cause VariantsToTable to write out NA values for missing fields instead of throwing an error. * will cause VariantsToTable to write out NA values for missing fields instead of throwing an error.
@ -294,6 +295,14 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
return x.toString(); return x.toString();
} }
}); });
getters.put("EVENTLENGTH", new Getter() { public String get(VariantContext vc) {
int maxLength = 0;
for ( final Allele a : vc.getAlternateAlleles() ) {
final int length = a.length() - vc.getReference().length();
if( Math.abs(length) > Math.abs(maxLength) ) { maxLength = length; }
}
return Integer.toString(maxLength);
}});
getters.put("QUAL", new Getter() { public String get(VariantContext vc) { return Double.toString(vc.getPhredScaledQual()); } }); getters.put("QUAL", new Getter() { public String get(VariantContext vc) { return Double.toString(vc.getPhredScaledQual()); } });
getters.put("TRANSITION", new Getter() { public String get(VariantContext vc) { getters.put("TRANSITION", new Getter() { public String get(VariantContext vc) {
if ( vc.isSNP() && vc.isBiallelic() ) if ( vc.isSNP() && vc.isBiallelic() )
@ -304,7 +313,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
getters.put("FILTER", new Getter() { public String get(VariantContext vc) { getters.put("FILTER", new Getter() { public String get(VariantContext vc) {
return vc.isNotFiltered() ? "PASS" : Utils.join(",", vc.getFilters()); } return vc.isNotFiltered() ? "PASS" : Utils.join(",", vc.getFilters()); }
}); });
getters.put("ID", new Getter() { public String get(VariantContext vc) { return vc.hasID() ? vc.getID() : "."; } });
getters.put("HET", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHetCount()); } }); getters.put("HET", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHetCount()); } });
getters.put("HOM-REF", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomRefCount()); } }); getters.put("HOM-REF", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomRefCount()); } });
getters.put("HOM-VAR", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomVarCount()); } }); getters.put("HOM-VAR", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomVarCount()); } });

19
public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java
View File

@ -46,7 +46,7 @@ public class SimpleTimer {
* @return the name associated with this timer * @return the name associated with this timer
*/ */
@Ensures("result != null") @Ensures("result != null")
public String getName() { public synchronized String getName() {
return name; return name;
} }
@ -58,7 +58,7 @@ public class SimpleTimer {
*/ */
@Requires("running == false") @Requires("running == false")
@Ensures({"result != null", "elapsed == 0l"}) @Ensures({"result != null", "elapsed == 0l"})
public SimpleTimer start() { public synchronized SimpleTimer start() {
elapsed = 0l; elapsed = 0l;
restart(); restart();
return this; return this;
@ -73,7 +73,7 @@ public class SimpleTimer {
*/ */
@Requires("running == false") @Requires("running == false")
@Ensures("result != null") @Ensures("result != null")
public SimpleTimer restart() { public synchronized SimpleTimer restart() {
running = true; running = true;
startTime = currentTime(); startTime = currentTime();
return this; return this;
@ -82,14 +82,14 @@ public class SimpleTimer {
/** /**
* @return is this timer running? * @return is this timer running?
*/ */
public boolean isRunning() { public synchronized boolean isRunning() {
return running; return running;
} }
/** /**
* @return A convenience function to obtain the current time in milliseconds from this timer * @return A convenience function to obtain the current time in milliseconds from this timer
*/ */
public long currentTime() { public synchronized long currentTime() {
return System.currentTimeMillis(); return System.currentTimeMillis();
} }
@ -101,7 +101,7 @@ public class SimpleTimer {
*/ */
@Requires("running == true") @Requires("running == true")
@Ensures({"result != null", "elapsed >= old(elapsed)", "running == false"}) @Ensures({"result != null", "elapsed >= old(elapsed)", "running == false"})
public SimpleTimer stop() { public synchronized SimpleTimer stop() {
running = false; running = false;
elapsed += currentTime() - startTime; elapsed += currentTime() - startTime;
return this; return this;
@ -116,12 +116,7 @@ public class SimpleTimer {
@Ensures({ @Ensures({
"result >= (elapsed/1000.0)", "result >= (elapsed/1000.0)",
"result >= 0"}) "result >= 0"})
public double getElapsedTime() { public synchronized double getElapsedTime() {
return (running ? (currentTime() - startTime + elapsed) : elapsed) / 1000.0; return (running ? (currentTime() - startTime + elapsed) : elapsed) / 1000.0;
} }
public void printElapsedTime(PrintStream out) {
out.printf("SimpleTimer %s: %.2f%n", name, getElapsedTime());
}
} }

3
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
View File

@ -381,7 +381,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
} }
} }
attributes.put(VariantContext.ID_KEY, id); if ( ! id.equals(VCFConstants.EMPTY_ID_FIELD) )
attributes.put(VariantContext.ID_KEY, id);
return attributes; return attributes;
} }

4
public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
View File

@ -111,6 +111,10 @@ public class UserException extends ReviewedStingException {
super(String.format("Couldn't read file because %s caused by %s", message, e.getMessage())); super(String.format("Couldn't read file because %s caused by %s", message, e.getMessage()));
} }
public CouldNotReadInputFile(File file) {
super(String.format("Couldn't read file %s", file.getAbsolutePath()));
}
public CouldNotReadInputFile(File file, String message) { public CouldNotReadInputFile(File file, String message) {
super(String.format("Couldn't read file %s because %s", file.getAbsolutePath(), message)); super(String.format("Couldn't read file %s because %s", file.getAbsolutePath(), message));
} }

2
public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
View File

@ -353,7 +353,7 @@ public class AlignmentUtils {
break; break;
case D: case D:
case N: case N:
refPos++; refPos += elementLength;
break; break;
case M: case M:
for ( int jjj = 0; jjj < elementLength; jjj++ ) { for ( int jjj = 0; jjj < elementLength; jjj++ ) {

2
public/java/test/org/broadinstitute/sting/MD5DB.java
View File

@ -239,7 +239,7 @@ public class MD5DB {
if ( ! expectedMD5.equals(filemd5sum) ) { if ( ! expectedMD5.equals(filemd5sum) ) {
// we are going to fail for real in assertEquals (so we are counted by the testing framework). // we are going to fail for real in assertEquals (so we are counted by the testing framework).
// prepare ourselves for the comparison // prepare ourselves for the comparison
System.out.printf("##### Test %s is going fail #####%n", name); System.out.printf("##### Test %s is going to fail #####%n", name);
String pathToExpectedMD5File = getMD5FilePath(expectedMD5, "[No DB file found]"); String pathToExpectedMD5File = getMD5FilePath(expectedMD5, "[No DB file found]");
String pathToFileMD5File = getMD5FilePath(filemd5sum, "[No DB file found]"); String pathToFileMD5File = getMD5FilePath(filemd5sum, "[No DB file found]");
System.out.printf("##### Path to expected file (MD5=%s): %s%n", expectedMD5, pathToExpectedMD5File); System.out.printf("##### Path to expected file (MD5=%s): %s%n", expectedMD5, pathToExpectedMD5File);

132
public/java/test/org/broadinstitute/sting/gatk/walkers/qc/TestVariantContextWalker.java 100755
View File

@ -0,0 +1,132 @@
/*
* Copyright (c) 2010 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.gatk.walkers.qc;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.PrintStream;
import java.util.Arrays;
import java.util.EnumSet;
import java.util.List;
/**
* Test routine for new VariantContext object
*/
@Reference(window=@Window(start=-20,stop=1))
public class TestVariantContextWalker extends RodWalker<Integer, Integer> {
@Output
PrintStream out;
@ArgumentCollection
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@Argument(fullName="takeFirstOnly", doc="Only take the first second at a locus, as opposed to all", required=false)
boolean takeFirstOnly = false;
@Argument(fullName="onlyContextsOfType", doc="Only take variant contexts of this type", required=false)
VariantContext.Type onlyOfThisType = null;
@Argument(fullName="onlyContextsStartinAtCurrentPosition", doc="Only take variant contexts at actually start at the current position, excluding those at span to the current location but start earlier", required=false)
boolean onlyContextsStartinAtCurrentPosition = false;
@Argument(fullName="printPerLocus", doc="If true, we'll print the variant contexts, in addition to counts", required=false)
boolean printContexts = false;
@Argument(fullName="outputVCF", doc="If provided, we'll convert the first input context into a VCF", required=false)
VCFWriter writer = null;
private boolean wroteHeader = false;
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( ref == null )
return 0;
else {
EnumSet<VariantContext.Type> allowedTypes = onlyOfThisType == null ? null : EnumSet.of(onlyOfThisType);
int n = 0;
List<VariantContext> contexts;
if ( onlyContextsStartinAtCurrentPosition )
contexts = tracker.getValues(variantCollection.variants, context.getLocation());
else // ! onlyContextsStartinAtCurrentPosition
contexts = tracker.getValues(variantCollection.variants);
for ( VariantContext vc : contexts ) {
if ( allowedTypes == null || allowedTypes.contains(vc.getType()) ) {
// we need to trigger decoding of the genotype string to pass integration tests
vc.getGenotypes();
if ( writer != null && n == 0 ) {
if ( ! wroteHeader ) {
writer.writeHeader(VariantContextAdaptors.createVCFHeader(null, vc));
wroteHeader = true;
}
writer.add(vc);
}
n++;
if ( printContexts ) out.printf(" %s%n", vc);
if ( takeFirstOnly ) break;
}
}
if ( n > 0 && printContexts ) {
out.printf("%s => had %d variant context objects%n", context.getLocation(), n);
out.printf("---------------------------------------------%n");
}
return n;
}
}
public Integer reduceInit() {
return 0;
}
public Integer reduce(Integer point, Integer sum) {
return point + sum;
}
@Override
public void onTraversalDone(Integer result) {
// Double check traversal result to make count is the same.
// TODO: Is this check necessary?
out.println("[REDUCE RESULT] Traversal result is: " + result);
}
}

4
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -89,7 +89,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@DataProvider(name = "trtestdata") @DataProvider(name = "trtestdata")
public Object[][] createTRTestData() { public Object[][] createTRTestData() {
new TRTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "2864f231fab7030377f3c8826796e48f" ); new TRTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "2864f231fab7030377f3c8826796e48f" );
new TRTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "c164dd635721ba6df3f06dac1877c32d"); new TRTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "d04cf1f6df486e45226ebfbf93a188a5");
new TRTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "74314e5562c1a65547bb0edaacffe602" ); new TRTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "74314e5562c1a65547bb0edaacffe602" );
new TRTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "2a37c6001826bfabf87063b1dfcf594f" ); new TRTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "2a37c6001826bfabf87063b1dfcf594f" );
return TRTest.getTests(TRTest.class); return TRTest.getTests(TRTest.class);
@ -200,7 +200,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test @Test
public void testTableRecalibratorSolidIndelsRemoveRefBias() { public void testTableRecalibratorSolidIndelsRemoveRefBias() {
HashMap<String, String> e = new HashMap<String, String>(); HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "7d5edb75b176e4151de225f699719ee4" ); e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "2ad4c17ac3ed380071137e4e53a398a5" );
for ( Map.Entry<String, String> entry : e.entrySet() ) { for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey(); String bam = entry.getKey();

21
public/java/test/org/broadinstitute/sting/utils/R/RScriptExecutorUnitTest.java
View File

@ -26,21 +26,12 @@ package org.broadinstitute.sting.utils.R;
import org.apache.commons.io.FileUtils; import org.apache.commons.io.FileUtils;
import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.walkers.diffengine.DiffElement;
import org.broadinstitute.sting.gatk.walkers.diffengine.DiffEngine;
import org.broadinstitute.sting.gatk.walkers.diffengine.DiffNode;
import org.broadinstitute.sting.gatk.walkers.diffengine.Difference;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test; import org.testng.annotations.Test;
import java.io.File; import java.io.File;
import java.io.IOException; import java.io.IOException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List; import java.util.List;
/** /**
@ -49,7 +40,6 @@ import java.util.List;
public class RScriptExecutorUnitTest extends BaseTest { public class RScriptExecutorUnitTest extends BaseTest {
final static String testrscript = "print(\"hello, world\")\n"; final static String testrscript = "print(\"hello, world\")\n";
final static String publicRScript = "plot_Tranches.R"; final static String publicRScript = "plot_Tranches.R";
final static String privateRScript = "variantCallQC.R";
// -------------------------------------------------------------------------------- // --------------------------------------------------------------------------------
// //
@ -74,17 +64,6 @@ public class RScriptExecutorUnitTest extends BaseTest {
@Test @Test
public void testPublic() { testOne(publicRScript, null, null, true); } public void testPublic() { testOne(publicRScript, null, null, true); }
@Test
public void testPrivate() { testOne(privateRScript, null, null, true); }
// make sure we don't break finding something in private by adding another directory
@Test
public void testPrivateWithAdditionalPath1() { testOne(privateRScript, null, "dist", true); }
// make sure we don't break finding something in private by adding another directory
@Test
public void testPrivateWithAdditionalPath2() { testOne(privateRScript, null, "doesNotExist", true); }
@Test(expectedExceptions = UserException.class) @Test(expectedExceptions = UserException.class)
public void testNonExistantScriptException() { testOne("does_not_exist.R", null, null, true); } public void testNonExistantScriptException() { testOne("does_not_exist.R", null, null, true); }

10
public/packages/GATKEngine.xml
View File

@ -26,14 +26,10 @@
<package name="GATKEngine"> <package name="GATKEngine">
<executable name="GATKEngine"> <executable name="GATKEngine">
<dependencies> <dependencies>
<!-- Core walkers --> <!-- Package everything in org.broadinstitute.sting -->
<package name="org.broadinstitute.sting.gatk.walkers.**" /> <package name="org.broadinstitute.sting.**" />
<!-- All non-oneoff GATK-specific RODs -->
<package name="org.broadinstitute.sting.utils.codecs.**" />
<!-- Filters -->
<package name="org.broadinstitute.sting.gatk.filters" />
<!-- Tribble codecs --> <!-- Tribble codecs -->
<package name="org.broad.tribble.*" /> <package name="org.broad.tribble.**" />
<!-- Workaround - depend on the logger impl required by JEXL --> <!-- Workaround - depend on the logger impl required by JEXL -->
<package name="org.apache.commons.logging.impl" /> <package name="org.apache.commons.logging.impl" />
</dependencies> </dependencies>

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

@ -36,8 +36,6 @@ class VcfGatherFunction extends CombineVariants with GatherFunction {
private lazy val originalGATK = this.originalFunction.asInstanceOf[CommandLineGATK] private lazy val originalGATK = this.originalFunction.asInstanceOf[CommandLineGATK]
override def freezeFieldValues { override def freezeFieldValues {
this.memoryLimit = Some(1)
this.jarFile = this.originalGATK.jarFile this.jarFile = this.originalGATK.jarFile
this.reference_sequence = this.originalGATK.reference_sequence this.reference_sequence = this.originalGATK.reference_sequence
this.intervals = this.originalGATK.intervals this.intervals = this.originalGATK.intervals