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Merge branch 'master' of github.com:broadinstitute/gsa-unstable

This commit is contained in:
Ryan Poplin 2012-12-03 10:08:56 -05:00
parent 1bdf17ef53 6f523a1ea0
commit 18b002c99c
42 changed files with 587 additions and 163 deletions
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97
build.xml
View File

@ -185,10 +185,7 @@
<include name="**/*.class"/> <include name="**/*.class"/>
</fileset> </fileset>
<patternset id="dependency.mask" includes="*.jar"> <patternset id="dependency.mask" includes="*.jar" />
<exclude name="testng*.jar" />
<exclude name="bcel*.jar" />
</patternset>
<path id="external.dependencies"> <path id="external.dependencies">
<fileset dir="${lib.dir}" erroronmissingdir="false"> <fileset dir="${lib.dir}" erroronmissingdir="false">
@ -205,6 +202,16 @@
<pathelement location="${scala.classes}" /> <pathelement location="${scala.classes}" />
</path> </path>
<path id="build.results">
<!-- Ensure that GenomeAnalysisTK.jar comes first in the path, as it contains overrides for certain classes in our dependencies -->
<pathelement location="${dist.dir}/GenomeAnalysisTK.jar" />
<!-- After GenomeAnalysisTK.jar we include all of the other jars in the dist directory -->
<fileset dir="${dist.dir}" erroronmissingdir="false">
<patternset refid="dependency.mask" />
<exclude name="GenomeAnalysisTK.jar" />
</fileset>
</path>
<fileset id="external.source.files" dir="${external.dir}" erroronmissingdir="false"> <fileset id="external.source.files" dir="${external.dir}" erroronmissingdir="false">
<include name="**/*.java" /> <include name="**/*.java" />
</fileset> </fileset>
@ -226,20 +233,20 @@
<!-- the path for resources that need to go into the GATK jar; <!-- the path for resources that need to go into the GATK jar;
any additional resources should go into this set. --> any additional resources should go into this set. -->
<path id="gatk.resources"> <path id="gatk.resources">
<fileset dir="${basedir}"> <fileset dir="${java.public.source.dir}">
<include name="${java.public.source.dir}/**/templates/*" /> <include name="**/resources/*" />
<include name="${java.private.source.dir}/**/templates/*" if="include.private" /> <include name="**/templates/*" />
<include name="${java.protected.source.dir}/**/templates/*" if="include.protected" /> </fileset>
<fileset dir="${java.private.source.dir}" erroronmissingdir="false">
<include name="**/resources/*" if="include.private" />
<include name="**/templates/*" if="include.private" />
</fileset>
<fileset dir="${java.protected.source.dir}" erroronmissingdir="false">
<include name="**/resources/*" if="include.protected" />
<include name="**/templates/*" if="include.protected" />
</fileset> </fileset>
</path> </path>
<path id="build.results">
<fileset dir="${dist.dir}">
<patternset refid="dependency.mask" />
</fileset>
</path>
<!-- ******************************************************************************** --> <!-- ******************************************************************************** -->
<!-- Ivy Retrieve --> <!-- Ivy Retrieve -->
<!-- ******************************************************************************** --> <!-- ******************************************************************************** -->
@ -672,6 +679,24 @@
</jar> </jar>
</target> </target>
<target name="na12878kb.jar" depends="gatk.compile,init.jar">
<jar jarfile="${dist.dir}/na12878kb.jar">
<fileset dir="${java.classes}">
<include name="org/broadinstitute/sting/utils/GenomeLocParser*.class"/>
<include name="org/broadinstitute/sting/utils/GenomeLoc.class"/>
<include name="org/broadinstitute/sting/utils/HasGenomeLocation.class"/>
<include name="org/broadinstitute/sting/utils/BaseUtils.class"/>
<include name="org/broadinstitute/sting/utils/Utils.class"/>
<include name="org/broadinstitute/sting/utils/exceptions/**/*.class"/>
<include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/**/*.class"/>
<include name="net/sf/picard/reference/FastaSequenceFile.class"/>
</fileset>
<fileset dir="${java.private.source.dir}">
<include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/resources/**/*"/>
</fileset>
</jar>
</target>
<target name="gatk.jar" depends="gatk.compile, init.jar, R.script.stage" description="generate the GATK distribution"> <target name="gatk.jar" depends="gatk.compile, init.jar, R.script.stage" description="generate the GATK distribution">
<jar jarfile="${dist.dir}/GenomeAnalysisTK.jar"> <jar jarfile="${dist.dir}/GenomeAnalysisTK.jar">
<path refid="gatk.resources"/> <path refid="gatk.resources"/>
@ -1103,15 +1128,10 @@
</path> </path>
<path id="testng.default.classpath"> <path id="testng.default.classpath">
<pathelement location="${java.classes}" /> <path refid="build.results" />
<pathelement location="${scala.classes}" />
<pathelement location="${java.contracts.dir}" /> <pathelement location="${java.contracts.dir}" />
<pathelement location="${java.test.classes}" /> <pathelement location="${java.test.classes}" />
<pathelement location="${scala.test.classes}" /> <pathelement location="${scala.test.classes}" />
<pathelement location="${R.tar.dir}" />
<path refid="R.script.source.path" />
<pathelement location="${key.dir}" />
<path refid="external.dependencies" />
</path> </path>
<!-- Test targets --> <!-- Test targets -->
@ -1119,9 +1139,6 @@
<target name="test.init.compile"> <target name="test.init.compile">
<mkdir dir="${java.test.classes}"/> <mkdir dir="${java.test.classes}"/>
<mkdir dir="${scala.test.classes}"/> <mkdir dir="${scala.test.classes}"/>
<antcall target="resolve">
<param name="ivy.conf" value="test"/>
</antcall>
</target> </target>
<target name="test.java.internal.compile" depends="dist,test.init.compile"> <target name="test.java.internal.compile" depends="dist,test.init.compile">
@ -1129,10 +1146,8 @@
<javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}"> <javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}">
<src refid="java.test.source.path" /> <src refid="java.test.source.path" />
<classpath> <classpath>
<path refid="external.dependencies" /> <path refid="build.results" />
<pathelement location="${java.classes}"/>
<pathelement location="${java.contracts.dir}"/> <pathelement location="${java.contracts.dir}"/>
<pathelement location="${testng.jar}"/>
</classpath> </classpath>
<compilerarg value="-proc:none"/> <compilerarg value="-proc:none"/>
</javac> </javac>
@ -1143,11 +1158,9 @@
<javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}" srcdir="${external.dir}"> <javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}" srcdir="${external.dir}">
<include name="*/test/**/*.java"/> <include name="*/test/**/*.java"/>
<classpath> <classpath>
<path refid="external.dependencies" /> <path refid="build.results" />
<pathelement location="${java.test.classes}"/> <pathelement location="${java.test.classes}"/>
<pathelement location="${java.classes}"/>
<pathelement location="${java.contracts.dir}"/> <pathelement location="${java.contracts.dir}"/>
<pathelement location="${testng.jar}"/>
</classpath> </classpath>
<compilerarg value="-proc:none"/> <compilerarg value="-proc:none"/>
</javac> </javac>
@ -1160,9 +1173,8 @@
<scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.test.classes}" deprecation="yes" unchecked="yes"> <scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.test.classes}" deprecation="yes" unchecked="yes">
<src refid="scala.test.source.path" /> <src refid="scala.test.source.path" />
<classpath> <classpath>
<path refid="scala.dependencies"/> <path refid="build.results"/>
<pathelement location="${java.test.classes}"/> <pathelement location="${java.test.classes}"/>
<pathelement location="${testng.jar}"/>
</classpath> </classpath>
</scalac> </scalac>
</target> </target>
@ -1369,14 +1381,13 @@
<!-- Fast test target that cuts major corners for speed. Requires that a full build has been done first. Java-only, single test class only --> <!-- Fast test target that cuts major corners for speed. Requires that a full build has been done first. Java-only, single test class only -->
<!-- Usage: ant fasttest -Dsingle=TestClass --> <!-- Usage: ant fasttest -Dsingle=TestClass -->
<target name="fasttest" depends="init.javaonly,init,test.init"> <target name="fasttest" depends="init.javaonly,init">
<condition property="not.clean"> <condition property="not.clean">
<and> <and>
<available file="${build.dir}" /> <available file="${build.dir}" />
<available file="${lib.dir}" /> <available file="${lib.dir}" />
<available file="${dist.dir}" /> <available file="${dist.dir}" />
<available file="${java.test.classes}" /> <available file="${java.test.classes}" />
<available file="${testng.jar}" />
</and> </and>
</condition> </condition>
<fail message="fasttest requires a NON-CLEAN working directory (INCLUDING test classes). Do a full test build using ant test.compile first." unless="not.clean" /> <fail message="fasttest requires a NON-CLEAN working directory (INCLUDING test classes). Do a full test build using ant test.compile first." unless="not.clean" />
@ -1394,13 +1405,27 @@
<javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}"> <javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}">
<src refid="java.test.source.path" /> <src refid="java.test.source.path" />
<classpath> <classpath>
<path refid="external.dependencies" />
<pathelement location="${java.classes}"/> <pathelement location="${java.classes}"/>
<pathelement location="${testng.jar}"/> <path refid="external.dependencies" />
</classpath> </classpath>
<compilerarg value="-proc:none"/> <compilerarg value="-proc:none"/>
</javac> </javac>
<!-- fasttest uses the unpackaged class files in its test classpath to avoid having to rebuild the jars in dist/ -->
<path id="testng.fasttest.classpath">
<pathelement location="${java.classes}" />
<pathelement location="${scala.classes}" />
<pathelement location="${java.contracts.dir}" />
<pathelement location="${java.test.classes}" />
<pathelement location="${scala.test.classes}" />
<pathelement location="${R.tar.dir}" />
<path refid="R.script.source.path" />
<pathelement location="${key.dir}" />
<path refid="external.dependencies" />
<path refid="java.source.path" /> <!-- Terrible hack to allow fasttest to see resource files stored in the source tree -->
</path>
<property name="testng.classpath" value="testng.fasttest.classpath" />
<run-test testtype="${single}" outputdir="${report}/${single}" runfailed="false"/> <run-test testtype="${single}" outputdir="${report}/${single}" runfailed="false"/>
</target> </target>
</project> </project>

11
ivy.xml
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@ -24,11 +24,8 @@
<ivy-module version="1.0"> <ivy-module version="1.0">
<info organisation="org.broadinstitute" module="Sting"/> <info organisation="org.broadinstitute" module="Sting"/>
<configurations defaultconfmapping="test->default"> <configurations>
<conf name="default" description="the core dependencies for the GATK"/> <conf name="default" description="the core dependencies for the GATK"/>
<conf name="test" extends="default" description="external dependencies used for testing and metrics"/>
<conf name="scala" extends="default" description="the dependencies for scala"/>
<conf name="queue" extends="scala" description="the dependencies for Queue"/>
</configurations> </configurations>
<dependencies defaultconf="default"> <dependencies defaultconf="default">
<dependency org="net.sf" name="sam" rev="latest.integration"/> <dependency org="net.sf" name="sam" rev="latest.integration"/>
@ -83,9 +80,9 @@
<dependency org="org.scala-lang" name="scala-library" rev="2.9.2"/> <dependency org="org.scala-lang" name="scala-library" rev="2.9.2"/>
<!-- testing and evaluation dependencies --> <!-- testing and evaluation dependencies -->
<dependency org="org.testng" name="testng" rev="5.14.1" conf="test"/> <dependency org="org.testng" name="testng" rev="5.14.1"/>
<dependency org="org.uncommons" name="reportng" rev="1.1.2" conf="test"/> <dependency org="org.uncommons" name="reportng" rev="1.1.2"/>
<dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT" conf="test"/> <dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT"/>
<!-- Contracts for Java and dependencies --> <!-- Contracts for Java and dependencies -->
<dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-r139"/> <dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-r139"/>

11
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
View File

@ -45,6 +45,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext; import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState;
import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult; import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult;
import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.codecs.vcf.*;
@ -292,9 +293,15 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
@Override @Override
public boolean includeReadsWithDeletionAtLoci() { return true; } public boolean includeReadsWithDeletionAtLoci() { return true; }
// enable non primary reads in the active region // enable non primary and extended reads in the active region
@Override @Override
public boolean wantsNonPrimaryReads() { return true; } public EnumSet<ActiveRegionReadState> desiredReadStates() {
return EnumSet.of(
ActiveRegionReadState.PRIMARY,
ActiveRegionReadState.NONPRIMARY,
ActiveRegionReadState.EXTENDED
);
}
@Override @Override
@Ensures({"result.isActiveProb >= 0.0", "result.isActiveProb <= 1.0"}) @Ensures({"result.isActiveProb >= 0.0", "result.isActiveProb <= 1.0"})

8
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -62,7 +62,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultipleSNPAlleles() { public void testMultipleSNPAlleles() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1, "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
Arrays.asList("704888987baacff8c7b273b8ab9938d0")); Arrays.asList("d20c7a143b899f0239bf64b652ad3edb"));
executeTest("test Multiple SNP alleles", spec); executeTest("test Multiple SNP alleles", spec);
} }
@ -197,7 +197,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test @Test
public void testOutputParameterAllSites() { public void testOutputParameterAllSites() {
testOutputParameters("--output_mode EMIT_ALL_SITES", "81fff490c0f59890f1e75dc290833434"); testOutputParameters("--output_mode EMIT_ALL_SITES", "8b26088a035e579c4afd3b46737291e4");
} }
private void testOutputParameters(final String args, final String md5) { private void testOutputParameters(final String args, final String md5) {
@ -345,13 +345,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSampleIndels1() { public void testMultiSampleIndels1() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1, baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
Arrays.asList("a4761d7f25e7a62f34494801c98a0da7")); Arrays.asList("69df7a00f800204564ca3726e1871132"));
List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst(); List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation + baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
"low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1, "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
Arrays.asList("c526c234947482d1cd2ffc5102083a08")); Arrays.asList("1256a7eceff2c2374c231ff981df486d"));
executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2); executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
} }

56
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java
View File

@ -2,16 +2,14 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.testng.Assert; import org.testng.Assert;
import org.testng.annotations.DataProvider; import org.testng.annotations.DataProvider;
import org.testng.annotations.Test; import org.testng.annotations.Test;
import java.util.ArrayList; import java.util.*;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
public class AFCalcResultUnitTest extends BaseTest { public class AFCalcResultUnitTest extends BaseTest {
private static class MyTest { private static class MyTest {
@ -79,4 +77,54 @@ public class AFCalcResultUnitTest extends BaseTest {
final double[] actualPosteriors = new double[]{result.getLog10PosteriorOfAFEq0(), result.getLog10PosteriorOfAFGT0()}; final double[] actualPosteriors = new double[]{result.getLog10PosteriorOfAFEq0(), result.getLog10PosteriorOfAFGT0()};
Assert.assertEquals(MathUtils.sumLog10(actualPosteriors), 1.0, 1e-3, "Posteriors don't sum to 1 with 1e-3 precision"); Assert.assertEquals(MathUtils.sumLog10(actualPosteriors), 1.0, 1e-3, "Posteriors don't sum to 1 with 1e-3 precision");
} }
@DataProvider(name = "TestIsPolymorphic")
public Object[][] makeTestIsPolymorphic() {
List<Object[]> tests = new ArrayList<Object[]>();
final List<Double> pValues = new LinkedList<Double>();
for ( final double p : Arrays.asList(0.01, 0.1, 0.9, 0.99, 0.999) )
for ( final double espilon : Arrays.asList(-1e-5, 0.0, 1e-5) )
pValues.add(p + espilon);
for ( final double pNonRef : pValues ) {
for ( final double pThreshold : pValues ) {
final boolean shouldBePoly = pNonRef >= pThreshold;
if ( pNonRef != pThreshold)
// let's not deal with numerical instability
tests.add(new Object[]{ pNonRef, pThreshold, shouldBePoly });
}
}
return tests.toArray(new Object[][]{});
}
private AFCalcResult makePolymorphicTestData(final double pNonRef) {
return new AFCalcResult(
new int[]{0},
1,
alleles,
MathUtils.normalizeFromLog10(new double[]{1 - pNonRef, pNonRef}, true, false),
log10Even,
Collections.singletonMap(C, Math.log10(pNonRef)));
}
@Test(enabled = true, dataProvider = "TestIsPolymorphic")
private void testIsPolymorphic(final double pNonRef, final double pThreshold, final boolean shouldBePoly) {
final AFCalcResult result = makePolymorphicTestData(pNonRef);
final boolean actualIsPoly = result.isPolymorphic(C, Math.log10(pThreshold));
Assert.assertEquals(actualIsPoly, shouldBePoly,
"isPolymorphic with pNonRef " + pNonRef + " and threshold " + pThreshold + " returned "
+ actualIsPoly + " but the expected result is " + shouldBePoly);
}
@Test(enabled = true, dataProvider = "TestIsPolymorphic")
private void testIsPolymorphicQual(final double pNonRef, final double pThreshold, final boolean shouldBePoly) {
final AFCalcResult result = makePolymorphicTestData(pNonRef);
final double qual = QualityUtils.phredScaleCorrectRate(pThreshold);
final boolean actualIsPoly = result.isPolymorphicPhredScaledQual(C, qual);
Assert.assertEquals(actualIsPoly, shouldBePoly,
"isPolymorphic with pNonRef " + pNonRef + " and threshold " + pThreshold + " returned "
+ actualIsPoly + " but the expected result is " + shouldBePoly);
}
} }

3
public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
View File

@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.ApplicationDetails; import org.broadinstitute.sting.utils.help.ApplicationDetails;
import org.broadinstitute.sting.utils.help.HelpFormatter; import org.broadinstitute.sting.utils.help.HelpFormatter;
import org.broadinstitute.sting.utils.help.HelpUtils;
import java.io.IOException; import java.io.IOException;
import java.util.*; import java.util.*;
@ -288,7 +289,7 @@ public abstract class CommandLineProgram {
*/ */
private static void printDocumentationReference() { private static void printDocumentationReference() {
errorPrintf("Visit our website and forum for extensive documentation and answers to %n"); errorPrintf("Visit our website and forum for extensive documentation and answers to %n");
errorPrintf("commonly asked questions http://www.broadinstitute.org/gatk%n"); errorPrintf("commonly asked questions " + HelpUtils.BASE_GATK_URL + "%n");
} }

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

@ -39,6 +39,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.ApplicationDetails; import org.broadinstitute.sting.utils.help.ApplicationDetails;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.GATKDocUtils; import org.broadinstitute.sting.utils.help.GATKDocUtils;
import org.broadinstitute.sting.utils.help.HelpUtils;
import org.broadinstitute.sting.utils.text.TextFormattingUtils; import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import java.util.*; import java.util.*;
@ -160,7 +161,7 @@ public class CommandLineGATK extends CommandLineExecutable {
List<String> header = new ArrayList<String>(); List<String> header = new ArrayList<String>();
header.add(String.format("The Genome Analysis Toolkit (GATK) v%s, Compiled %s",getVersionNumber(), getBuildTime())); header.add(String.format("The Genome Analysis Toolkit (GATK) v%s, Compiled %s",getVersionNumber(), getBuildTime()));
header.add("Copyright (c) 2010 The Broad Institute"); header.add("Copyright (c) 2010 The Broad Institute");
header.add("For support and documentation go to http://www.broadinstitute.org/gatk"); header.add("For support and documentation go to " + HelpUtils.BASE_GATK_URL);
return header; return header;
} }

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

@ -30,12 +30,10 @@ import net.sf.samtools.*;
import net.sf.samtools.util.CloseableIterator; import net.sf.samtools.util.CloseableIterator;
import net.sf.samtools.util.RuntimeIOException; import net.sf.samtools.util.RuntimeIOException;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.downsampling.*;
import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
import org.broadinstitute.sting.gatk.downsampling.DownsamplingMethod;
import org.broadinstitute.sting.gatk.ReadMetrics; import org.broadinstitute.sting.gatk.ReadMetrics;
import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.downsampling.*;
import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator; import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator;
import org.broadinstitute.sting.gatk.filters.ReadFilter; import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.iterators.*; import org.broadinstitute.sting.gatk.iterators.*;
@ -567,7 +565,7 @@ public class SAMDataSource {
* *
* @return the start positions of the first chunk of reads for all BAM files * @return the start positions of the first chunk of reads for all BAM files
*/ */
public Map<SAMReaderID, GATKBAMFileSpan> getInitialReaderPositions() { protected Map<SAMReaderID, GATKBAMFileSpan> getInitialReaderPositions() {
Map<SAMReaderID, GATKBAMFileSpan> initialPositions = new HashMap<SAMReaderID, GATKBAMFileSpan>(); Map<SAMReaderID, GATKBAMFileSpan> initialPositions = new HashMap<SAMReaderID, GATKBAMFileSpan>();
SAMReaders readers = resourcePool.getAvailableReaders(); SAMReaders readers = resourcePool.getAvailableReaders();
@ -585,7 +583,7 @@ public class SAMDataSource {
* @param shard The shard specifying the data limits. * @param shard The shard specifying the data limits.
* @return An iterator over the selected data. * @return An iterator over the selected data.
*/ */
public StingSAMIterator getIterator( Shard shard ) { protected StingSAMIterator getIterator( Shard shard ) {
return getIterator(resourcePool.getAvailableReaders(), shard, shard instanceof ReadShard); return getIterator(resourcePool.getAvailableReaders(), shard, shard instanceof ReadShard);
} }

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

@ -25,11 +25,9 @@
package org.broadinstitute.sting.gatk.filters; package org.broadinstitute.sting.gatk.filters;
import com.google.common.base.Function;
import com.google.common.collect.Collections2;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.help.GATKDocUtils; import org.broadinstitute.sting.utils.help.GATKDocUtils;
import org.broadinstitute.sting.utils.help.HelpUtils;
import java.util.Collection; import java.util.Collection;
import java.util.List; import java.util.List;
@ -73,7 +71,7 @@ public class FilterManager extends PluginManager<ReadFilter> {
return String.format("Read filter %s not found. Available read filters:%n%n%s%n%n%s",pluginName, return String.format("Read filter %s not found. Available read filters:%n%n%s%n%n%s",pluginName,
userFriendlyListofReadFilters(availableFilters), userFriendlyListofReadFilters(availableFilters),
"Please consult the GATK Documentation (http://www.broadinstitute.org/gatk/gatkdocs/) for more information."); "Please consult the GATK Documentation (" + HelpUtils.GATK_DOCS_URL + ") for more information.");
} }
private String userFriendlyListofReadFilters(List<Class<? extends ReadFilter>> filters) { private String userFriendlyListofReadFilters(List<Class<? extends ReadFilter>> filters) {

16
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
View File

@ -258,13 +258,23 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
activeRegion.add( read ); activeRegion.add( read );
} }
for( final ActiveRegion otherRegionToTest : workQueue ) { for( final ActiveRegion otherRegionToTest : workQueue ) {
if( !bestRegion.equals(otherRegionToTest) && otherRegionToTest.getExtendedLoc().overlapsP( readLoc ) ) { if( !bestRegion.equals(otherRegionToTest) ) {
otherRegionToTest.add( read ); // check for non-primary vs. extended
if ( otherRegionToTest.getLocation().overlapsP( readLoc ) ) {
otherRegionToTest.add( read );
} else if ( walker.wantsExtendedReads() && otherRegionToTest.getExtendedLoc().overlapsP( readLoc ) ) {
otherRegionToTest.add( read );
}
} }
} }
} }
placedReads.add( read ); placedReads.add( read );
} else if( activeRegion.getExtendedLoc().overlapsP( readLoc ) && walker.wantsNonPrimaryReads() ) { // check for non-primary vs. extended
} else if( activeRegion.getLocation().overlapsP( readLoc ) ) {
if ( walker.wantsNonPrimaryReads() ) {
activeRegion.add( read );
}
} else if( walker.wantsExtendedReads() && activeRegion.getExtendedLoc().overlapsP( readLoc )) {
activeRegion.add( read ); activeRegion.add( read );
} }
} }

22
public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
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@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.walkers; package org.broadinstitute.sting.gatk.walkers;
import com.google.java.contract.Ensures;
import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broad.tribble.Feature; import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Input;
@ -13,14 +14,14 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.activeregion.ActiveRegion; import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState;
import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult; import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult;
import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
import org.broadinstitute.sting.utils.interval.IntervalSetRule; import org.broadinstitute.sting.utils.interval.IntervalSetRule;
import org.broadinstitute.sting.utils.interval.IntervalUtils; import org.broadinstitute.sting.utils.interval.IntervalUtils;
import java.io.PrintStream; import java.io.PrintStream;
import java.util.ArrayList; import java.util.*;
import java.util.List;
/** /**
* Base class for all the Active Region Walkers. * Base class for all the Active Region Walkers.
@ -70,11 +71,24 @@ public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<Map
return true; // We are keeping all the reads return true; // We are keeping all the reads
} }
public boolean wantsNonPrimaryReads() { public EnumSet<ActiveRegionReadState> desiredReadStates() {
return false; return EnumSet.of(ActiveRegionReadState.PRIMARY);
}
public final boolean wantsNonPrimaryReads() {
return desiredReadStates().contains(ActiveRegionReadState.NONPRIMARY);
}
public boolean wantsExtendedReads() {
return desiredReadStates().contains(ActiveRegionReadState.EXTENDED);
}
public boolean wantsUnmappedReads() {
return desiredReadStates().contains(ActiveRegionReadState.UNMAPPED);
} }
// Determine probability of active status over the AlignmentContext // Determine probability of active status over the AlignmentContext
@Ensures({"result.isActiveProb >= 0.0", "result.isActiveProb <= 1.0"})
public abstract ActivityProfileResult isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context); public abstract ActivityProfileResult isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context);
// Map over the ActiveRegion // Map over the ActiveRegion

1
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
View File

@ -282,6 +282,7 @@ public class DiffEngine {
// now that we have a specific list of values we want to show, display them // now that we have a specific list of values we want to show, display them
GATKReport report = new GATKReport(); GATKReport report = new GATKReport();
final String tableName = "differences"; final String tableName = "differences";
// TODO for Geraldine -- link needs to be updated below
report.addTable(tableName, "Summarized differences between the master and test files. See http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine for more information", 3); report.addTable(tableName, "Summarized differences between the master and test files. See http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine for more information", 3);
final GATKReportTable table = report.getTable(tableName); final GATKReportTable table = report.getTable(tableName);
table.addColumn("Difference"); table.addColumn("Difference");

3
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java
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@ -138,7 +138,8 @@ public class DiffObjects extends RodWalker<Integer, Integer> {
/** /**
* Writes out a file of the DiffEngine format: * Writes out a file of the DiffEngine format:
* *
* http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine * TODO for Geraldine -- link needs to be updated below (and also in SelectVariants and RefSeqCodec GATK docs)
* http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine
*/ */
@Output(doc="File to which results should be written",required=true) @Output(doc="File to which results should be written",required=true)
protected PrintStream out; protected PrintStream out;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -382,11 +382,9 @@ public class UnifiedGenotyperEngine {
if ( alternateAllele.isReference() ) if ( alternateAllele.isReference() )
continue; continue;
// we are non-ref if the probability of being non-ref > the emit confidence. // Compute if the site is considered polymorphic with sufficient confidence relative to our
// the emit confidence is phred-scaled, say 30 => 10^-3. // phred-scaled emission QUAL
// the posterior AF > 0 is log10: -5 => 10^-5 final boolean isNonRef = AFresult.isPolymorphicPhredScaledQual(alternateAllele, UAC.STANDARD_CONFIDENCE_FOR_EMITTING);
// we are non-ref if 10^-5 < 10^-3 => -5 < -3
final boolean isNonRef = AFresult.isPolymorphic(alternateAllele, UAC.STANDARD_CONFIDENCE_FOR_EMITTING / -10.0);
// if the most likely AC is not 0, then this is a good alternate allele to use // if the most likely AC is not 0, then this is a good alternate allele to use
if ( isNonRef ) { if ( isNonRef ) {

11
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java
View File

@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
import com.google.java.contract.Ensures; import com.google.java.contract.Ensures;
import com.google.java.contract.Requires; import com.google.java.contract.Requires;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Allele;
@ -234,10 +235,20 @@ public class AFCalcResult {
* *
* @return true if there's enough confidence (relative to log10minPNonRef) to reject AF == 0 * @return true if there's enough confidence (relative to log10minPNonRef) to reject AF == 0
*/ */
@Requires("MathUtils.goodLog10Probability(log10minPNonRef)")
public boolean isPolymorphic(final Allele allele, final double log10minPNonRef) { public boolean isPolymorphic(final Allele allele, final double log10minPNonRef) {
return getLog10PosteriorOfAFGt0ForAllele(allele) >= log10minPNonRef; return getLog10PosteriorOfAFGt0ForAllele(allele) >= log10minPNonRef;
} }
/**
* Same as #isPolymorphic but takes a phred-scaled quality score as input
*/
public boolean isPolymorphicPhredScaledQual(final Allele allele, final double minPNonRefPhredScaledQual) {
if ( minPNonRefPhredScaledQual < 0 ) throw new IllegalArgumentException("phredScaledQual " + minPNonRefPhredScaledQual + " < 0 ");
final double log10Threshold = Math.log10(QualityUtils.qualToProb(minPNonRefPhredScaledQual));
return isPolymorphic(allele, log10Threshold);
}
/** /**
* Are any of the alleles polymorphic w.r.t. #isPolymorphic? * Are any of the alleles polymorphic w.r.t. #isPolymorphic?
* *

9
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
View File

@ -95,7 +95,8 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) @DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingStats> { public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingStats> {
private static final boolean DEBUG = false; @Argument(fullName="debug", shortName="debug", doc="If specified, print out very verbose debug information (if -l DEBUG is also specified)", required = false)
protected boolean DEBUG = false;
/** /**
* The VCF file we are phasing variants from. * The VCF file we are phasing variants from.
* *
@ -949,7 +950,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
} }
if (DEBUG) logger.debug("\nPhasing table [AFTER CALCULATION]:\n" + sampleHaps + "\n"); if (DEBUG) logger.debug("\nPhasing table [AFTER CALCULATION]:\n" + sampleHaps + "\n");
MaxHaplotypeAndQuality maxHapQual = new MaxHaplotypeAndQuality(sampleHaps, true); MaxHaplotypeAndQuality maxHapQual = new MaxHaplotypeAndQuality(sampleHaps, DEBUG);
double posteriorProb = maxHapQual.maxEntry.getScore().getValue(); double posteriorProb = maxHapQual.maxEntry.getScore().getValue();
if (DEBUG) if (DEBUG)
@ -971,7 +972,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
public MaxHaplotypeAndQuality(PhasingTable hapTable, boolean printDebug) { public MaxHaplotypeAndQuality(PhasingTable hapTable, boolean printDebug) {
// Marginalize each haplotype to its first 2 positions: // Marginalize each haplotype to its first 2 positions:
hapTable = HaplotypeTableCreator.marginalizeAsNewTable(hapTable); hapTable = HaplotypeTableCreator.marginalizeAsNewTable(hapTable);
if (DEBUG && printDebug) if (printDebug)
logger.debug("\nPhasing table [AFTER MAPPING]:\n" + hapTable + "\n"); logger.debug("\nPhasing table [AFTER MAPPING]:\n" + hapTable + "\n");
calculateMaxHapAndPhasingQuality(hapTable, printDebug); calculateMaxHapAndPhasingQuality(hapTable, printDebug);
@ -981,7 +982,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
private void calculateMaxHapAndPhasingQuality(PhasingTable hapTable, boolean printDebug) { private void calculateMaxHapAndPhasingQuality(PhasingTable hapTable, boolean printDebug) {
hapTable.normalizeScores(); hapTable.normalizeScores();
if (DEBUG && printDebug) if (printDebug)
logger.debug("\nPhasing table [AFTER NORMALIZATION]:\n" + hapTable + "\n"); logger.debug("\nPhasing table [AFTER NORMALIZATION]:\n" + hapTable + "\n");
// Determine the phase at this position: // Determine the phase at this position:

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
View File

@ -13,7 +13,7 @@ import java.util.Set;
/** /**
* Stratifies the eval RODs by user-supplied JEXL expressions * Stratifies the eval RODs by user-supplied JEXL expressions
* *
* See http://www.broadinstitute.org/gsa/wiki/index.php/Using_JEXL_expressions for more details * See http://gatkforums.broadinstitute.org/discussion/1255/what-are-jexl-expressions-and-how-can-i-use-them-with-the-gatk for more details
*/ */
public class JexlExpression extends VariantStratifier implements StandardStratification { public class JexlExpression extends VariantStratifier implements StandardStratification {
// needs to know the jexl expressions // needs to know the jexl expressions

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

@ -32,6 +32,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.HelpUtils;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList; import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
@ -80,7 +81,7 @@ public class VariantDataManager {
final double theSTD = standardDeviation(theMean, iii); final double theSTD = standardDeviation(theMean, iii);
logger.info( annotationKeys.get(iii) + String.format(": \t mean = %.2f\t standard deviation = %.2f", theMean, theSTD) ); logger.info( annotationKeys.get(iii) + String.format(": \t mean = %.2f\t standard deviation = %.2f", theMean, theSTD) );
if( Double.isNaN(theMean) ) { if( Double.isNaN(theMean) ) {
throw new UserException.BadInput("Values for " + annotationKeys.get(iii) + " annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See http://www.broadinstitute.org/gsa/wiki/index.php/VariantAnnotator"); throw new UserException.BadInput("Values for " + annotationKeys.get(iii) + " annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See " + HelpUtils.GATK_FORUM_URL + "discussion/49/using-variant-annotator");
} }
foundZeroVarianceAnnotation = foundZeroVarianceAnnotation || (theSTD < 1E-6); foundZeroVarianceAnnotation = foundZeroVarianceAnnotation || (theSTD < 1E-6);

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

@ -51,8 +51,7 @@ import java.util.*;
* The Variant Validation Assessor is a tool for vetting/assessing validation data (containing genotypes). * The Variant Validation Assessor is a tool for vetting/assessing validation data (containing genotypes).
* The tool produces a VCF that is annotated with information pertaining to plate quality control and by * The tool produces a VCF that is annotated with information pertaining to plate quality control and by
* default is soft-filtered by high no-call rate or low Hardy-Weinberg probability. * default is soft-filtered by high no-call rate or low Hardy-Weinberg probability.
* If you have .ped files, please first convert them to VCF format * If you have .ped files, please first convert them to VCF format.
* (see http://www.broadinstitute.org/gsa/wiki/index.php/Converting_ped_to_vcf).
* *
* <h2>Input</h2> * <h2>Input</h2>
* <p> * <p>

18
public/java/src/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSession.java
View File

@ -210,13 +210,23 @@ public class JnaSession implements Session {
} }
public static void setAttribute(Pointer jt, String name, String value) throws DrmaaException { public static void setAttribute(Pointer jt, String name, String value) throws DrmaaException {
checkError(LibDrmaa.drmaa_set_attribute(jt, name, value, getError(), LibDrmaa.DRMAA_ERROR_STRING_BUFFER_LEN)); if (getAttrNames().contains(name)) {
checkError(LibDrmaa.drmaa_set_attribute(jt, name, value, getError(), LibDrmaa.DRMAA_ERROR_STRING_BUFFER_LEN));
}
else {
throw new InvalidAttributeValueException("Attribute " + name + " is not supported by this implementation of DRMAA");
}
} }
public static String getAttribute(Pointer jt, String name) throws DrmaaException { public static String getAttribute(Pointer jt, String name) throws DrmaaException {
Memory attrBuffer = new Memory(LibDrmaa.DRMAA_ATTR_BUFFER); if (getAttrNames().contains(name)) {
checkError(LibDrmaa.drmaa_get_attribute(jt, name, attrBuffer, LibDrmaa.DRMAA_ATTR_BUFFER_LEN, getError(), LibDrmaa.DRMAA_ERROR_STRING_BUFFER_LEN)); Memory attrBuffer = new Memory(LibDrmaa.DRMAA_ATTR_BUFFER);
return attrBuffer.getString(0); checkError(LibDrmaa.drmaa_get_attribute(jt, name, attrBuffer, LibDrmaa.DRMAA_ATTR_BUFFER_LEN, getError(), LibDrmaa.DRMAA_ERROR_STRING_BUFFER_LEN));
return attrBuffer.getString(0);
}
else {
throw new InvalidAttributeValueException("Attribute " + name + " is not supported by this implementation of DRMAA");
}
} }
public static void setVectorAttribute(Pointer jt, String name, Collection<String> values) throws DrmaaException { public static void setVectorAttribute(Pointer jt, String name, Collection<String> values) throws DrmaaException {

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

@ -374,7 +374,7 @@ public final class GenomeLocParser {
int start = 1; int start = 1;
int stop = -1; int stop = -1;
final int colonIndex = str.indexOf(":"); final int colonIndex = str.lastIndexOf(":");
if(colonIndex == -1) { if(colonIndex == -1) {
contig = str.substring(0, str.length()); // chr1 contig = str.substring(0, str.length()); // chr1
stop = Integer.MAX_VALUE; stop = Integer.MAX_VALUE;

2
public/java/src/org/broadinstitute/sting/utils/QualityUtils.java
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@ -9,7 +9,7 @@ import net.sf.samtools.SAMUtils;
* @author Kiran Garimella * @author Kiran Garimella
*/ */
public class QualityUtils { public class QualityUtils {
public final static byte MAX_RECALIBRATED_Q_SCORE = 93; public final static byte MAX_RECALIBRATED_Q_SCORE = SAMUtils.MAX_PHRED_SCORE;
public final static byte MAX_QUAL_SCORE = SAMUtils.MAX_PHRED_SCORE; public final static byte MAX_QUAL_SCORE = SAMUtils.MAX_PHRED_SCORE;
public final static double ERROR_RATE_OF_MAX_QUAL_SCORE = qualToErrorProbRaw(MAX_QUAL_SCORE); public final static double ERROR_RATE_OF_MAX_QUAL_SCORE = qualToErrorProbRaw(MAX_QUAL_SCORE);

16
public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegionReadState.java 100644
View File

@ -0,0 +1,16 @@
package org.broadinstitute.sting.utils.activeregion;
/**
* Created with IntelliJ IDEA.
* User: thibault
* Date: 11/26/12
* Time: 2:35 PM
*
* Describes how a read relates to an assigned ActiveRegion
*/
public enum ActiveRegionReadState {
PRIMARY, // This is the read's primary region
NONPRIMARY, // This region overlaps the read, but it is not primary
EXTENDED, // This region would overlap the read if it were extended
UNMAPPED // This read is not mapped
}

13
public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java
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@ -406,10 +406,15 @@ public class BAQ {
// so BQi = Qi - BAQi + 64 // so BQi = Qi - BAQi + 64
byte[] bqTag = new byte[baq.length]; byte[] bqTag = new byte[baq.length];
for ( int i = 0; i < bqTag.length; i++) { for ( int i = 0; i < bqTag.length; i++) {
int bq = (int)read.getBaseQualities()[i] + 64; final int bq = (int)read.getBaseQualities()[i] + 64;
int baq_i = (int)baq[i]; final int baq_i = (int)baq[i];
int tag = bq - baq_i; final int tag = bq - baq_i;
if ( tag < 0 ) throw new ReviewedStingException("BAQ tag calculation error. BAQ value above base quality at " + read); // problem with the calculation of the correction factor; this is our problem
if ( tag < 0 )
throw new ReviewedStingException("BAQ tag calculation error. BAQ value above base quality at " + read);
// the original quality is too high, almost certainly due to using the wrong encoding in the BAM file
if ( tag > Byte.MAX_VALUE )
throw new UserException.MalformedBAM(read, "we encountered an extremely high quality score (" + (bq - 64) + ") with BAQ correction factor of " + baq_i + "; the BAM file appears to be using the wrong encoding for quality scores");
bqTag[i] = (byte)tag; bqTag[i] = (byte)tag;
} }
return new String(bqTag); return new String(bqTag);

5
public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
View File

@ -30,6 +30,7 @@ import net.sf.samtools.SAMSequenceDictionary;
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport; import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpUtils;
import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@ -267,7 +268,7 @@ public class UserException extends ReviewedStingException {
public static class ReadMissingReadGroup extends MalformedBAM { public static class ReadMissingReadGroup extends MalformedBAM {
public ReadMissingReadGroup(SAMRecord read) { public ReadMissingReadGroup(SAMRecord read) {
super(read, String.format("Read %s is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK. Please use http://www.broadinstitute.org/gsa/wiki/index.php/ReplaceReadGroups to fix this problem", read.getReadName())); super(read, String.format("Read %s is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK. Please use " + HelpUtils.GATK_FORUM_URL + "discussion/59/companion-utilities-replacereadgroups to fix this problem", read.getReadName()));
} }
} }
@ -343,7 +344,7 @@ public class UserException extends ReviewedStingException {
super(String.format("Lexicographically sorted human genome sequence detected in %s." super(String.format("Lexicographically sorted human genome sequence detected in %s."
+ "\nFor safety's sake the GATK requires human contigs in karyotypic order: 1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M either leading or trailing these contigs." + "\nFor safety's sake the GATK requires human contigs in karyotypic order: 1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M either leading or trailing these contigs."
+ "\nThis is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files." + "\nThis is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files."
+ "\nYou can use the ReorderSam utility to fix this problem: http://www.broadinstitute.org/gsa/wiki/index.php/ReorderSam" + "\nYou can use the ReorderSam utility to fix this problem: " + HelpUtils.GATK_FORUM_URL + "discussion/58/companion-utilities-reordersam"
+ "\n %s contigs = %s", + "\n %s contigs = %s",
name, name, ReadUtils.prettyPrintSequenceRecords(dict))); name, name, ReadUtils.prettyPrintSequenceRecords(dict)));
} }

8
public/java/src/org/broadinstitute/sting/utils/help/ForumAPIUtils.java
View File

@ -44,14 +44,13 @@ public class ForumAPIUtils {
/** /**
* How we post to the forum * How we post to the forum
*/ */
private final static String API_URL = "https://gatkforums.broadinstitute.org/api/v1/";
final private static String ACCESS_TOKEN = "access_token="; final private static String ACCESS_TOKEN = "access_token=";
public static List<String> getPostedTools(String forumKey) { public static List<String> getPostedTools(String forumKey) {
Gson gson = new Gson(); Gson gson = new Gson();
List<String> output = new ArrayList<String>(); List<String> output = new ArrayList<String>();
String text = httpGet(API_URL + "categories.json?CategoryIdentifier=tool-bulletin&page=1-100000&" + ACCESS_TOKEN + forumKey); String text = httpGet(HelpUtils.GATK_FORUM_API_URL + "categories.json?CategoryIdentifier=tool-bulletin&page=1-100000&" + ACCESS_TOKEN + forumKey);
APIQuery details = gson.fromJson(text, APIQuery.class); APIQuery details = gson.fromJson(text, APIQuery.class);
ForumDiscussion[] discussions = details.Discussions; ForumDiscussion[] discussions = details.Discussions;
@ -159,7 +158,7 @@ public class ForumAPIUtils {
Gson gson = new Gson(); Gson gson = new Gson();
String data = gson.toJson(post.getPostData()); String data = gson.toJson(post.getPostData());
httpPost(data, API_URL + "post/discussion.json?" + ACCESS_TOKEN + forumKey); httpPost(data, HelpUtils.GATK_FORUM_API_URL + "post/discussion.json?" + ACCESS_TOKEN + forumKey);
} }
@ -167,8 +166,7 @@ public class ForumAPIUtils {
class APIQuery { class APIQuery {
ForumDiscussion[] Discussions; ForumDiscussion[] Discussions;
public APIQuery() { public APIQuery() {}
}
} }
} }

2
public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java
View File

@ -28,7 +28,7 @@ public class GATKDocUtils {
/** /**
* The URL root for RELEASED GATKDOC units * The URL root for RELEASED GATKDOC units
*/ */
public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gatk/gatkdocs/"; public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = HelpUtils.GATK_DOCS_URL;
/** /**
* The URL root for STABLE GATKDOC units * The URL root for STABLE GATKDOC units
*/ */

9
public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java
View File

@ -32,6 +32,15 @@ import org.broadinstitute.sting.utils.classloader.JVMUtils;
import java.lang.reflect.Field; import java.lang.reflect.Field;
public class HelpUtils { public class HelpUtils {
public final static String BASE_GATK_URL = "http://www.broadinstitute.org/gatk";
public final static String GATK_DOCS_URL = BASE_GATK_URL + "/gatkdocs/";
public final static String GATK_FORUM_URL = "http://gatkforums.broadinstitute.org/";
public final static String GATK_FORUM_API_URL = "https://gatkforums.broadinstitute.org/api/v1/";
protected static boolean assignableToClass(ProgramElementDoc classDoc, Class lhsClass, boolean requireConcrete) { protected static boolean assignableToClass(ProgramElementDoc classDoc, Class lhsClass, boolean requireConcrete) {
try { try {
Class type = getClassForDoc(classDoc); Class type = getClassForDoc(classDoc);

14
public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
View File

@ -652,23 +652,19 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
PerSamplePileupElementTracker<PE> tracker = (PerSamplePileupElementTracker<PE>) pileupElementTracker; PerSamplePileupElementTracker<PE> tracker = (PerSamplePileupElementTracker<PE>) pileupElementTracker;
PerSamplePileupElementTracker<PE> filteredTracker = new PerSamplePileupElementTracker<PE>(); PerSamplePileupElementTracker<PE> filteredTracker = new PerSamplePileupElementTracker<PE>();
int current = 0;
for (final String sample : tracker.getSamples()) { for (final String sample : tracker.getSamples()) {
PileupElementTracker<PE> perSampleElements = tracker.getElements(sample); PileupElementTracker<PE> perSampleElements = tracker.getElements(sample);
List<PileupElement> filteredPileup = new ArrayList<PileupElement>(); int current = 0;
for (PileupElement p : perSampleElements) { UnifiedPileupElementTracker<PE> filteredPileup = new UnifiedPileupElementTracker<PE>();
for (PE p : perSampleElements) {
if (positions.contains(current)) if (positions.contains(current))
filteredPileup.add(p); filteredPileup.add(p);
} current++;
if (!filteredPileup.isEmpty()) {
AbstractReadBackedPileup<RBP, PE> pileup = createNewPileup(loc, perSampleElements);
filteredTracker.addElements(sample, pileup.pileupElementTracker);
} }
filteredTracker.addElements(sample, filteredPileup);
current++;
} }
return (RBP) createNewPileup(loc, filteredTracker); return (RBP) createNewPileup(loc, filteredTracker);

64
public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java 100644
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@ -0,0 +1,64 @@
package org.broadinstitute.sting.utils.recalibration.covariates;
import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.TandemRepeat;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.recalibration.ReadCovariates;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import java.util.Arrays;
/**
* Created with IntelliJ IDEA.
* User: rpoplin
* Date: 11/3/12
*/
public class RepeatLengthCovariate implements ExperimentalCovariate {
final int MAX_REPEAT_LENGTH = 20;
// Initialize any member variables using the command-line arguments passed to the walkers
@Override
public void initialize(final RecalibrationArgumentCollection RAC) {}
@Override
public void recordValues(final GATKSAMRecord read, final ReadCovariates values) {
byte[] readBytes = read.getReadBases();
for (int i = 0; i < readBytes.length; i++) {
int maxRL = 0;
for (int str = 1; str <= 8; str++) {
if (i + str <= readBytes.length) {
maxRL = Math.max(maxRL, VariantContextUtils.findNumberofRepetitions(
Arrays.copyOfRange(readBytes,i,i + str),
Arrays.copyOfRange(readBytes,i,readBytes.length)
));
}
}
if(maxRL > MAX_REPEAT_LENGTH) { maxRL = MAX_REPEAT_LENGTH; }
values.addCovariate(maxRL, maxRL, maxRL, i);
}
}
// Used to get the covariate's value from input csv file during on-the-fly recalibration
@Override
public final Object getValue(final String str) {
return Byte.parseByte(str);
}
@Override
public String formatKey(final int key) {
return String.format("%d", key);
}
@Override
public int keyFromValue(final Object value) {
return (value instanceof String) ? Integer.parseInt((String) value) : (Integer) value;
}
@Override
public int maximumKeyValue() {
return MAX_REPEAT_LENGTH + 1;
}
}

2
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
View File

@ -1267,7 +1267,7 @@ public class VariantContextUtils {
* @param testString String to test * @param testString String to test
* @return Number of repetitions (0 if testString is not a concatenation of n repeatUnit's * @return Number of repetitions (0 if testString is not a concatenation of n repeatUnit's
*/ */
protected static int findNumberofRepetitions(byte[] repeatUnit, byte[] testString) { public static int findNumberofRepetitions(byte[] repeatUnit, byte[] testString) {
int numRepeats = 0; int numRepeats = 0;
for (int start = 0; start < testString.length; start += repeatUnit.length) { for (int start = 0; start < testString.length; start += repeatUnit.length) {
int end = start + repeatUnit.length; int end = start + repeatUnit.length;

1
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/SortingVariantContextWriterBase.java
View File

@ -71,7 +71,6 @@ abstract class SortingVariantContextWriterBase implements VariantContextWriter {
this.takeOwnershipOfInner = takeOwnershipOfInner; this.takeOwnershipOfInner = takeOwnershipOfInner;
// has to be PriorityBlockingQueue to be thread-safe // has to be PriorityBlockingQueue to be thread-safe
// see http://getsatisfaction.com/gsa/topics/missing_loci_output_in_multi_thread_mode_when_implement_sortingvcfwriterbase?utm_content=topic_link&utm_medium=email&utm_source=new_topic
this.queue = new PriorityBlockingQueue<VCFRecord>(50, new VariantContextComparator()); this.queue = new PriorityBlockingQueue<VCFRecord>(50, new VariantContextComparator());
this.mostUpstreamWritableLoc = BEFORE_MOST_UPSTREAM_LOC; this.mostUpstreamWritableLoc = BEFORE_MOST_UPSTREAM_LOC;

251
public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
View File

@ -1,6 +1,8 @@
package org.broadinstitute.sting.gatk.traversals; package org.broadinstitute.sting.gatk.traversals;
import com.google.java.contract.PreconditionError;
import net.sf.samtools.*; import net.sf.samtools.*;
import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState;
import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
import org.broadinstitute.sting.utils.interval.IntervalUtils; import org.broadinstitute.sting.utils.interval.IntervalUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@ -23,6 +25,7 @@ import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult; import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.testng.Assert; import org.testng.Assert;
import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test; import org.testng.annotations.Test;
@ -45,6 +48,8 @@ public class TraverseActiveRegionsTest extends BaseTest {
private class DummyActiveRegionWalker extends ActiveRegionWalker<Integer, Integer> { private class DummyActiveRegionWalker extends ActiveRegionWalker<Integer, Integer> {
private final double prob; private final double prob;
private EnumSet<ActiveRegionReadState> states = super.desiredReadStates();
protected List<GenomeLoc> isActiveCalls = new ArrayList<GenomeLoc>(); protected List<GenomeLoc> isActiveCalls = new ArrayList<GenomeLoc>();
protected Map<GenomeLoc, ActiveRegion> mappedActiveRegions = new HashMap<GenomeLoc, ActiveRegion>(); protected Map<GenomeLoc, ActiveRegion> mappedActiveRegions = new HashMap<GenomeLoc, ActiveRegion>();
@ -52,6 +57,20 @@ public class TraverseActiveRegionsTest extends BaseTest {
this.prob = 1.0; this.prob = 1.0;
} }
public DummyActiveRegionWalker(double constProb) {
this.prob = constProb;
}
public DummyActiveRegionWalker(EnumSet<ActiveRegionReadState> wantStates) {
this.prob = 1.0;
this.states = wantStates;
}
@Override
public EnumSet<ActiveRegionReadState> desiredReadStates() {
return states;
}
@Override @Override
public ActivityProfileResult isActive(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public ActivityProfileResult isActive(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
isActiveCalls.add(ref.getLocus()); isActiveCalls.add(ref.getLocus());
@ -82,7 +101,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
private GenomeLocParser genomeLocParser; private GenomeLocParser genomeLocParser;
private List<GenomeLoc> intervals; private List<GenomeLoc> intervals;
private List<SAMRecord> reads; private List<GATKSAMRecord> reads;
@BeforeClass @BeforeClass
private void init() throws FileNotFoundException { private void init() throws FileNotFoundException {
@ -96,21 +115,21 @@ public class TraverseActiveRegionsTest extends BaseTest {
intervals.add(genomeLocParser.createGenomeLoc("1", 1000, 1999)); intervals.add(genomeLocParser.createGenomeLoc("1", 1000, 1999));
intervals.add(genomeLocParser.createGenomeLoc("1", 2000, 2999)); intervals.add(genomeLocParser.createGenomeLoc("1", 2000, 2999));
intervals.add(genomeLocParser.createGenomeLoc("1", 10000, 20000)); intervals.add(genomeLocParser.createGenomeLoc("1", 10000, 20000));
// TODO: this fails! intervals.add(genomeLocParser.createGenomeLoc("20", 10000, 10100));
//intervals.add(genomeLocParser.createGenomeLoc("20", 10000, 20000));
intervals = IntervalUtils.sortAndMergeIntervals(genomeLocParser, intervals, IntervalMergingRule.OVERLAPPING_ONLY).toList(); intervals = IntervalUtils.sortAndMergeIntervals(genomeLocParser, intervals, IntervalMergingRule.OVERLAPPING_ONLY).toList();
reads = new ArrayList<SAMRecord>(); reads = new ArrayList<GATKSAMRecord>();
reads.add(buildSAMRecord("simple", "1", 100, 200)); reads.add(buildSAMRecord("simple", "1", 100, 200));
reads.add(buildSAMRecord("overlap_equal", "1", 10, 20)); reads.add(buildSAMRecord("overlap_equal", "1", 10, 20));
reads.add(buildSAMRecord("overlap_unequal", "1", 10, 21)); reads.add(buildSAMRecord("overlap_unequal", "1", 10, 21));
reads.add(buildSAMRecord("boundary_equal", "1", 1990, 2009)); reads.add(buildSAMRecord("boundary_equal", "1", 1990, 2009));
reads.add(buildSAMRecord("boundary_unequal", "1", 1995, 2050)); reads.add(buildSAMRecord("boundary_unequal", "1", 1990, 2008));
reads.add(buildSAMRecord("extended_only", "1", 3000, 3100));
reads.add(buildSAMRecord("extended_and_np", "1", 990, 1990)); reads.add(buildSAMRecord("extended_and_np", "1", 990, 1990));
reads.add(buildSAMRecord("outside_intervals", "1", 5000, 6000)); reads.add(buildSAMRecord("outside_intervals", "1", 5000, 6000));
// TODO reads.add(buildSAMRecord("simple20", "20", 10025, 10075));
//reads.add(buildSAMRecord("simple20", "20", 10100, 10150));
// required by LocusIteratorByState, and I prefer to list them in test case order above
ReadUtils.sortReadsByCoordinate(reads);
} }
@Test @Test
@ -134,6 +153,18 @@ public class TraverseActiveRegionsTest extends BaseTest {
return activeIntervals; return activeIntervals;
} }
@Test (expectedExceptions = PreconditionError.class)
public void testIsActiveRangeLow () {
DummyActiveRegionWalker walker = new DummyActiveRegionWalker(-0.1);
getActiveRegions(walker, intervals).values();
}
@Test (expectedExceptions = PreconditionError.class)
public void testIsActiveRangeHigh () {
DummyActiveRegionWalker walker = new DummyActiveRegionWalker(1.1);
getActiveRegions(walker, intervals).values();
}
@Test @Test
public void testActiveRegionCoverage() { public void testActiveRegionCoverage() {
DummyActiveRegionWalker walker = new DummyActiveRegionWalker(); DummyActiveRegionWalker walker = new DummyActiveRegionWalker();
@ -187,80 +218,210 @@ public class TraverseActiveRegionsTest extends BaseTest {
} }
@Test @Test
public void testReadMapping() { public void testPrimaryReadMapping() {
DummyActiveRegionWalker walker = new DummyActiveRegionWalker(); DummyActiveRegionWalker walker = new DummyActiveRegionWalker();
// Contract: Each read has the Primary state in a single region (or none) // Contract: Each read has the Primary state in a single region (or none)
// This is the region of maximum overlap for the read (earlier if tied) // This is the region of maximum overlap for the read (earlier if tied)
// simple: Primary in 1:1-999
// overlap_equal: Primary in 1:1-999
// overlap_unequal: Primary in 1:1-999
// boundary_equal: Non-Primary in 1:1000-1999, Primary in 1:2000-2999
// boundary_unequal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999
// extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999
// outside_intervals: none
// simple20: Primary in 20:10000-10100
Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals);
ActiveRegion region;
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1, 999));
getRead(region, "simple");
getRead(region, "overlap_equal");
getRead(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
getRead(region, "boundary_unequal");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
getRead(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
getRead(region, "simple20");
// TODO: more tests and edge cases
}
@Test
public void testNonPrimaryReadMapping() {
DummyActiveRegionWalker walker = new DummyActiveRegionWalker(
EnumSet.of(ActiveRegionReadState.PRIMARY, ActiveRegionReadState.NONPRIMARY));
// Contract: Each read has the Primary state in a single region (or none)
// This is the region of maximum overlap for the read (earlier if tied)
// Contract: Each read has the Non-Primary state in all other regions it overlaps
// simple: Primary in 1:1-999
// overlap_equal: Primary in 1:1-999
// overlap_unequal: Primary in 1:1-999
// boundary_equal: Non-Primary in 1:1000-1999, Primary in 1:2000-2999
// boundary_unequal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999
// extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999
// outside_intervals: none
// simple20: Primary in 20:10000-10100
Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals);
ActiveRegion region;
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1, 999));
getRead(region, "simple");
getRead(region, "overlap_equal");
getRead(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
getRead(region, "boundary_equal");
getRead(region, "boundary_unequal");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
getRead(region, "boundary_equal");
getRead(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
getRead(region, "simple20");
// TODO: more tests and edge cases
}
@Test
public void testExtendedReadMapping() {
DummyActiveRegionWalker walker = new DummyActiveRegionWalker(
EnumSet.of(ActiveRegionReadState.PRIMARY, ActiveRegionReadState.NONPRIMARY, ActiveRegionReadState.EXTENDED));
// Contract: Each read has the Primary state in a single region (or none)
// This is the region of maximum overlap for the read (earlier if tied)
// Contract: Each read has the Non-Primary state in all other regions it overlaps // Contract: Each read has the Non-Primary state in all other regions it overlaps
// Contract: Each read has the Extended state in regions where it only overlaps if the region is extended // Contract: Each read has the Extended state in regions where it only overlaps if the region is extended
// simple: Primary in 1:1-999 // simple: Primary in 1:1-999
// overlap_equal: Primary in 1:1-999 // overlap_equal: Primary in 1:1-999
// overlap_unequal: Primary in 1:1-999 // overlap_unequal: Primary in 1:1-999
// boundary_equal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999 // boundary_equal: Non-Primary in 1:1000-1999, Primary in 1:2000-2999
// boundary_unequal: Non-Primary in 1:1000-1999, Primary in 1:2000-2999 // boundary_unequal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999
// extended_only: Extended in 1:2000-2999
// extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999 // extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999
// outside_intervals: none // outside_intervals: none
// simple20: Primary in 20:10000-10100
// TODO
// simple20: Primary in 20:10000-20000
Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals); Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals);
ActiveRegion region; ActiveRegion region;
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1, 999)); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1, 999));
verifyReadPrimary(region, "simple"); getRead(region, "simple");
verifyReadPrimary(region, "overlap_equal"); getRead(region, "overlap_equal");
verifyReadPrimary(region, "overlap_unequal"); getRead(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal"); verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal"); verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_only"); getRead(region, "extended_and_np");
// TODO: fail verifyReadNonPrimary(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals"); verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999)); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999));
verifyReadNotPlaced(region, "simple"); verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal"); verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal"); verifyReadNotPlaced(region, "overlap_unequal");
// TODO: fail verifyReadPrimary(region, "boundary_equal"); getRead(region, "boundary_equal");
// TODO: fail verifyReadNonPrimary(region, "boundary_unequal"); getRead(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_only"); getRead(region, "extended_and_np");
// TODO: fail verifyReadPrimary(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals"); verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999)); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
verifyReadNotPlaced(region, "simple"); verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal"); verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal"); verifyReadNotPlaced(region, "overlap_unequal");
// TODO: fail verifyReadNonPrimary(region, "boundary_equal"); getRead(region, "boundary_equal");
verifyReadPrimary(region, "boundary_unequal"); getRead(region, "boundary_unequal");
// TODO: fail verifyReadExtended(region, "extended_only"); getRead(region, "extended_and_np");
// TODO: fail verifyReadExtended(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals"); verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
getRead(region, "simple20");
// TODO: more tests and edge cases // TODO: more tests and edge cases
} }
private void verifyReadPrimary(ActiveRegion region, String readName) {
SAMRecord read = getRead(region, readName);
Assert.assertFalse(read.getNotPrimaryAlignmentFlag(), "Read " + read + " not primary in active region " + region);
}
private void verifyReadNonPrimary(ActiveRegion region, String readName) {
SAMRecord read = getRead(region, readName);
Assert.assertTrue(read.getNotPrimaryAlignmentFlag(), "Read " + read + " primary in active region " + region);
}
private void verifyReadExtended(ActiveRegion region, String readName) {
Assert.fail("The Extended read state has not been implemented");
}
private void verifyReadNotPlaced(ActiveRegion region, String readName) { private void verifyReadNotPlaced(ActiveRegion region, String readName) {
for (SAMRecord read : region.getReads()) { for (SAMRecord read : region.getReads()) {
if (read.getReadName().equals(readName)) if (read.getReadName().equals(readName))
@ -274,7 +435,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
return read; return read;
} }
Assert.fail("Read " + readName + " not found in active region " + region); Assert.fail("Read " + readName + " not assigned to active region " + region);
return null; return null;
} }
@ -282,6 +443,8 @@ public class TraverseActiveRegionsTest extends BaseTest {
for (LocusShardDataProvider dataProvider : createDataProviders(intervals)) for (LocusShardDataProvider dataProvider : createDataProviders(intervals))
t.traverse(walker, dataProvider, 0); t.traverse(walker, dataProvider, 0);
t.endTraversal(walker, 0);
return walker.mappedActiveRegions; return walker.mappedActiveRegions;
} }
@ -345,7 +508,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
engine.setGenomeLocParser(genomeLocParser); engine.setGenomeLocParser(genomeLocParser);
t.initialize(engine); t.initialize(engine);
StingSAMIterator iterator = ArtificialSAMUtils.createReadIterator(reads); StingSAMIterator iterator = ArtificialSAMUtils.createReadIterator(new ArrayList<SAMRecord>(reads));
Shard shard = new MockLocusShard(genomeLocParser, intervals); Shard shard = new MockLocusShard(genomeLocParser, intervals);
List<LocusShardDataProvider> providers = new ArrayList<LocusShardDataProvider>(); List<LocusShardDataProvider> providers = new ArrayList<LocusShardDataProvider>();

19
public/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java
View File

@ -2,6 +2,8 @@ package org.broadinstitute.sting.utils;
import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.SAMSequenceRecord;
import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
@ -74,6 +76,23 @@ public class GenomeLocParserUnitTest extends BaseTest {
genomeLocParser.parseGenomeLoc("Bad:0-1"); genomeLocParser.parseGenomeLoc("Bad:0-1");
} }
@Test
public void testContigHasColon() {
SAMFileHeader header = new SAMFileHeader();
header.setSortOrder(net.sf.samtools.SAMFileHeader.SortOrder.coordinate);
SAMSequenceDictionary dict = new SAMSequenceDictionary();
SAMSequenceRecord rec = new SAMSequenceRecord("c:h:r1", 10);
rec.setSequenceLength(10);
dict.addSequence(rec);
header.setSequenceDictionary(dict);
final GenomeLocParser myGenomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
GenomeLoc loc = myGenomeLocParser.parseGenomeLoc("c:h:r1:4-5");
assertEquals(0, loc.getContigIndex());
assertEquals(loc.getStart(), 4);
assertEquals(loc.getStop(), 5);
}
@Test @Test
public void testParseGoodString() { public void testParseGoodString() {
GenomeLoc loc = genomeLocParser.parseGenomeLoc("chr1:1-10"); GenomeLoc loc = genomeLocParser.parseGenomeLoc("chr1:1-10");

1
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
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@ -28,7 +28,6 @@ public class VCFIntegrationTest extends WalkerTest {
} }
@Test(enabled = true) @Test(enabled = true)
// See https://getsatisfaction.com/gsa/topics/support_vcf_4_1_structural_variation_breakend_alleles?utm_content=topic_link&utm_medium=email&utm_source=new_topic
public void testReadingAndWritingBreakpointAlleles() { public void testReadingAndWritingBreakpointAlleles() {
String testVCF = privateTestDir + "breakpoint-example.vcf"; String testVCF = privateTestDir + "breakpoint-example.vcf";

2
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
View File

@ -793,7 +793,7 @@ public class VariantContextUtilsUnitTest extends BaseTest {
int sampleI = 0; int sampleI = 0;
for ( final List<Allele> alleles : Utils.makePermutations(vc.getAlleles(), 2, true) ) { for ( final List<Allele> alleles : Utils.makePermutations(vc.getAlleles(), 2, true) ) {
genotypes.add(GenotypeBuilder.create("sample" + sampleI, alleles)); genotypes.add(GenotypeBuilder.create("sample" + sampleI++, alleles));
} }
genotypes.add(GenotypeBuilder.createMissing("missing", 2)); genotypes.add(GenotypeBuilder.createMissing("missing", 2));

3
public/packages/GATKEngine.xml
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@ -36,6 +36,9 @@
<dir name="org/broadinstitute/sting/utils/R" includes="**/*.tar.gz" /> <dir name="org/broadinstitute/sting/utils/R" includes="**/*.tar.gz" />
<!-- All R scripts in org.broadinstitute.sting --> <!-- All R scripts in org.broadinstitute.sting -->
<dir name="org/broadinstitute/sting" includes="**/*.R" /> <dir name="org/broadinstitute/sting" includes="**/*.R" />
<!-- Resources in org.broadinstitute.sting -->
<dir name="org/broadinstitute/sting" includes="**/resources/*" />
<dir name="org/broadinstitute/sting" includes="**/templates/*" />
<!-- The GATK public key --> <!-- The GATK public key -->
<file path="GATK_public.key" /> <file path="GATK_public.key" />
</dependencies> </dependencies>

4
public/scala/src/org/broadinstitute/sting/queue/QSettings.scala
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@ -72,6 +72,10 @@ class QSettings {
@Argument(fullName="resident_memory_request_parameter", shortName="resMemReqParam", doc="Parameter for resident memory requests. By default not requested.", required=false) @Argument(fullName="resident_memory_request_parameter", shortName="resMemReqParam", doc="Parameter for resident memory requests. By default not requested.", required=false)
var residentRequestParameter: String = _ var residentRequestParameter: String = _
@Argument(fullName="job_walltime", shortName="wallTime", doc="Setting the required DRMAA walltime or LSF run limit.", required=false)
@ClassType(classOf[Long])
var jobWalltime: Option[Long] = None
/** The name of the parallel environment (required for SGE, for example) */ /** The name of the parallel environment (required for SGE, for example) */
@Argument(fullName="job_parallel_env", shortName="jobParaEnv", doc="An SGE style parallel environment to use for jobs requesting more than 1 core. Equivalent to submitting jobs with -pe ARG nt for jobs with nt > 1", required=false) @Argument(fullName="job_parallel_env", shortName="jobParaEnv", doc="An SGE style parallel environment to use for jobs requesting more than 1 core. Equivalent to submitting jobs with -pe ARG nt for jobs with nt > 1", required=false)
var parallelEnvironmentName: String = "smp_pe" // Broad default var parallelEnvironmentName: String = "smp_pe" // Broad default

3
public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala
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@ -65,6 +65,9 @@ class DrmaaJobRunner(val session: Session, val function: CommandLineFunction) ex
drmaaJob.setJoinFiles(true) drmaaJob.setJoinFiles(true)
} }
if(!function.wallTime.isEmpty)
drmaaJob.setHardWallclockTimeLimit(function.wallTime.get)
drmaaJob.setNativeSpecification(functionNativeSpec) drmaaJob.setNativeSpecification(functionNativeSpec)
// Instead of running the function.commandLine, run "sh <jobScript>" // Instead of running the function.commandLine, run "sh <jobScript>"

7
public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala
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@ -151,8 +151,11 @@ class Lsf706JobRunner(val function: CommandLineFunction) extends CommandLineJobR
throw new QException("setOption_() returned -1 while setting esub"); throw new QException("setOption_() returned -1 while setting esub");
} }
// LSF specific: get the max runtime for the jobQueue and pass it for this job if(!function.wallTime.isEmpty)
request.rLimits(LibLsf.LSF_RLIMIT_RUN) = Lsf706JobRunner.getRlimitRun(function.jobQueue) request.rLimits(LibLsf.LSF_RLIMIT_RUN) = function.wallTime.get.toInt
else
// LSF specific: get the max runtime for the jobQueue and pass it for this job
request.rLimits(LibLsf.LSF_RLIMIT_RUN) = Lsf706JobRunner.getRlimitRun(function.jobQueue)
// Run the command as sh <jobScript> // Run the command as sh <jobScript>
request.command = "sh " + jobScript request.command = "sh " + jobScript

10
public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala
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@ -33,6 +33,9 @@ import org.broadinstitute.sting.commandline.Argument
trait CommandLineFunction extends QFunction with Logging { trait CommandLineFunction extends QFunction with Logging {
def commandLine: String def commandLine: String
/** Setting the wall time request for DRMAA / run limit for LSF */
var wallTime: Option[Long] = None
/** Upper memory limit */ /** Upper memory limit */
@Argument(doc="Memory limit", required=false) @Argument(doc="Memory limit", required=false)
var memoryLimit: Option[Double] = None var memoryLimit: Option[Double] = None
@ -67,6 +70,9 @@ trait CommandLineFunction extends QFunction with Logging {
super.copySettingsTo(function) super.copySettingsTo(function)
function match { function match {
case commandLineFunction: CommandLineFunction => case commandLineFunction: CommandLineFunction =>
if(commandLineFunction.wallTime.isEmpty)
commandLineFunction.wallTime = this.wallTime
if (commandLineFunction.memoryLimit.isEmpty) if (commandLineFunction.memoryLimit.isEmpty)
commandLineFunction.memoryLimit = this.memoryLimit commandLineFunction.memoryLimit = this.memoryLimit
@ -110,6 +116,10 @@ trait CommandLineFunction extends QFunction with Logging {
* Sets all field values. * Sets all field values.
*/ */
override def freezeFieldValues() { override def freezeFieldValues() {
if(wallTime.isEmpty)
wallTime = qSettings.jobWalltime
if (jobQueue == null) if (jobQueue == null)
jobQueue = qSettings.jobQueue jobQueue = qSettings.jobQueue

11
public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
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@ -126,4 +126,15 @@ class HelloWorldPipelineTest {
spec.jobRunners = Seq("GridEngine") spec.jobRunners = Seq("GridEngine")
PipelineTest.executeTest(spec) PipelineTest.executeTest(spec)
} }
// disabled because our DRMAA implementation doesn't support wallTime
@Test(enabled=false, timeOut=36000000)
def testHelloWorldWithWalltime() {
val spec = new PipelineTestSpec
spec.name = "HelloWorldWithWalltime"
spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" +
" -wallTime 100"
spec.jobRunners = PipelineTest.allJobRunners
PipelineTest.executeTest(spec)
}
} }