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Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable

This commit is contained in:
Chris Hartl 2012-12-26 09:20:32 -05:00
parent 5780926254 64c3a0ff62
commit f2b7c6f0e1
379 changed files with 4533 additions and 3366 deletions
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88
build.xml
View File

@ -107,6 +107,12 @@
<!-- To run tests with debugging, use -Dtest.debug=true -Dtest.debug.port=XXXX on the command line -->
<property name="test.debug.port" value="5005" /> <!-- override on the command line if desired -->
<property name="test.default.maxmemory" value="4g"/>
<!-- clover parameters -->
<property name="clover.jar" location="private/resources/clover/lib/clover.jar"/>
<property name="clover.instrument.level" location="method"/>
<taskdef resource="cloverlib.xml" classpath="${clover.jar}"/>
<!-- ******************************************************************************** -->
@ -267,19 +273,19 @@
<!-- Comment out the following lines to build the GATK without a network connection, assuming you have all of the libraries cached already -->
<get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}"
dest="${ivy.jar.dir}/${ivy.jar.file}"
usetimestamp="true"/>
<taskdef resource="org/apache/ivy/ant/antlib.xml"
uri="antlib:org.apache.ivy.ant"
classpath="${ivy.jar.dir}/${ivy.jar.file}"/>
<!-- <get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}" -->
<!-- dest="${ivy.jar.dir}/${ivy.jar.file}" -->
<!-- usetimestamp="true"/> -->
<!-- <taskdef resource="org/apache/ivy/ant/antlib.xml" -->
<!-- uri="antlib:org.apache.ivy.ant" -->
<!-- classpath="${ivy.jar.dir}/${ivy.jar.file}"/> -->
<get src="http://repo1.maven.org/maven2/org/apache/maven/maven-ant-tasks/${maven-ant-tasks.install.version}/${maven-ant-tasks.jar.file}"
dest="${ivy.jar.dir}/${maven-ant-tasks.jar.file}"
usetimestamp="true"/>
<taskdef resource="org/apache/maven/artifact/ant/antlib.xml"
uri="antlib:antlib:org.apache.maven.artifact.ant"
classpath="${ivy.jar.dir}/${maven-ant-tasks.jar.file}"/>
<!-- <get src="http://repo1.maven.org/maven2/org/apache/maven/maven-ant-tasks/${maven-ant-tasks.install.version}/${maven-ant-tasks.jar.file}" -->
<!-- dest="${ivy.jar.dir}/${maven-ant-tasks.jar.file}" -->
<!-- usetimestamp="true"/> -->
<!-- <taskdef resource="org/apache/maven/artifact/ant/antlib.xml" -->
<!-- uri="antlib:antlib:org.apache.maven.artifact.ant" -->
<!-- classpath="${ivy.jar.dir}/${maven-ant-tasks.jar.file}"/> -->
<!-- End network lines -->
@ -596,6 +602,7 @@
<path id="doclet.classpath">
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />
<pathelement location="${clover.jar}" />
</path>
<javadoc doclet="org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet"
@ -644,12 +651,8 @@
<target name="sting-utils.jar" depends="gatk.compile, init.jar, R.public.tar, R.script.stage">
<jar jarfile="${dist.dir}/StingUtils.jar">
<fileset dir="${java.classes}">
<include name="**/utils/**/*.class"/>
<exclude name="**/utils/codecs/vcf/**/*.class"/>
<exclude name="**/utils/variantcontext/**/*.class"/>
</fileset>
<fileset dir="${java.classes}" includes="**/commandline/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/utils/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/commandline/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/pipeline/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/tools/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/jna/**/*.class"/>
@ -659,7 +662,7 @@
<include name="**/${R.package.path}/**/*.tar.gz"/>
</fileset>
<fileset dir="${R.script.staging.dir}">
<include name="**/utils/**/*.R"/>
<include name="**/sting/utils/**/*.R"/>
</fileset>
<manifest>
<attribute name="Premain-Class" value="org.broadinstitute.sting.utils.instrumentation.Sizeof" />
@ -667,14 +670,10 @@
</jar>
</target>
<target name="vcf.jar" depends="gatk.compile,init.jar">
<jar jarfile="${dist.dir}/vcf.jar">
<target name="variant.jar" depends="gatk.compile,init.jar">
<jar jarfile="${dist.dir}/variant.jar">
<fileset dir="${java.classes}">
<include name="org/broadinstitute/sting/utils/codecs/vcf/**/*.class"/>
<include name="org/broadinstitute/sting/utils/codecs/bcf2/**/*.class"/>
<include name="org/broadinstitute/sting/utils/variantcontext/**/*.class"/>
<include name="org/broadinstitute/sting/utils/exceptions/**"/>
<include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>
<include name="org/broadinstitute/variant/**/*.class"/>
</fileset>
</jar>
</target>
@ -685,7 +684,7 @@
<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/variant/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"/>
@ -703,12 +702,12 @@
<fileset dir="${java.contracts.dir}" />
<fileset dir="${java.classes}">
<include name="${resource.file}" />
<include name="**/gatk/**/*.class" />
<include name="**/alignment/**/*.class"/>
<include name="**/sting/gatk/**/*.class" />
<include name="**/sting/alignment/**/*.class"/>
</fileset>
<fileset dir="${R.script.staging.dir}">
<include name="**/gatk/**/*.R"/>
<include name="**/alignment/**/*.R"/>
<include name="**/sting/gatk/**/*.R"/>
<include name="**/sting/alignment/**/*.R"/>
</fileset>
<fileset dir="${key.dir}">
<include name="**/*.key"/>
@ -719,7 +718,7 @@
</jar>
<jar jarfile="${dist.dir}/Aligner.jar">
<fileset dir="${java.classes}" includes="**/alignment/**/*.class" />
<fileset dir="${java.classes}" includes="**/sting/alignment/**/*.class" />
</jar>
<subant target="dist" genericantfile="build.xml">
@ -755,7 +754,7 @@
</jar>
</target>
<target name="sting.jar" depends="sting-utils.jar, vcf.jar, gatk.jar, queue.jar" />
<target name="sting.jar" depends="sting-utils.jar, variant.jar, gatk.jar, queue.jar" />
<target name="init.manifests" depends="sting.jar">
<pathconvert property="jar.classpath" pathsep=" ">
@ -1098,7 +1097,6 @@
<property name="iwww.report.dir" value="${user.home}/private_html/report"/>
<property name="test.output" value="${dist.dir}/test"/>
<property name="testng.jar" value="${lib.dir}/testng-5.14.1.jar"/>
<property name="test.maxmemory" value="4g"/> <!-- provide a ceiling on the memory that unit/integration tests can consume. -->
<path id="java.test.source.path">
<dirset dir="${basedir}">
@ -1129,6 +1127,7 @@
<path id="testng.default.classpath">
<path refid="build.results" />
<pathelement path="${clover.jar}"/>
<pathelement location="${java.contracts.dir}" />
<pathelement location="${java.test.classes}" />
<pathelement location="${scala.test.classes}" />
@ -1136,6 +1135,21 @@
<!-- Test targets -->
<target name="clover.clean">
<clover-clean/>
</target>
<target name="clover.report">
<clover-html-report outdir="clover_html" title="GATK Clover report"/>
</target>
<target name="with.clover">
<clover-setup fullyQualifyJavaLang="true" instrumentationLevel="${clover.instrument.level}">
</clover-setup>
<property name="compile.scala" value="false" /> <!-- currently doesn't work with scala -->
<property name="test.maxmemory" value="32g"/> <!-- clover requires lots of memory -->
</target>
<target name="test.init.compile">
<mkdir dir="${java.test.classes}"/>
<mkdir dir="${scala.test.classes}"/>
@ -1215,6 +1229,7 @@
<echo message="Test Classpath: ${test.classpath.display.string}" />
<echo message="" />
<echo message="Sting: Running @{testtype} test cases!"/>
<echo message="Test Memory : ${test.maxmemory}" />
<!-- no test is allowed to run for more than 10 hours -->
<taskdef resource="testngtasks" classpath="${testng.jar}"/>
@ -1228,10 +1243,11 @@
listeners="org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.sting.TestNGTestTransformer,org.broadinstitute.sting.StingTextReporter,org.uncommons.reportng.HTMLReporter">
<jvmarg value="-Xmx${test.maxmemory}" />
<jvmarg value="-ea" />
<jvmarg value="-Dclover.pertest.coverage=diff" />
<jvmarg value="-Djava.awt.headless=true" />
<jvmarg value="-Dpipeline.run=${pipeline.run}" />
<jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
<jvmarg line="${cofoja.jvm.args}"/>
<!-- <jvmarg line="${cofoja.jvm.args}"/> -->
<jvmarg line="${debug.jvm.args}"/>
<!-- NOTE: To run tests with debugging, use -Dtest.debug=true -Dtest.debug.port=XXXX on the command line -->
@ -1270,6 +1286,7 @@
<target name="test.init">
<property name="testng.classpath" value="testng.default.classpath" />
<property name="test.maxmemory" value="${test.default.maxmemory}"/>
</target>
<target name="init.testgatkjar">
@ -1382,6 +1399,7 @@
<!-- Fast test target that cuts major corners for speed. Requires that a full build has been done first. Java-only, single test class only -->
<!-- Usage: ant fasttest -Dsingle=TestClass -->
<target name="fasttest" depends="init.javaonly,init">
<property name="test.maxmemory" value="${test.default.maxmemory}"/>
<condition property="not.clean">
<and>
<available file="${build.dir}" />

3
protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java
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@ -30,7 +30,8 @@ import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.pileup.*;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.variantcontext.Allele;
import java.io.PrintStream;
import java.util.*;

75
protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AdvancedRecalibrationEngine.java
View File

@ -25,51 +25,46 @@ package org.broadinstitute.sting.gatk.walkers.bqsr;
* OTHER DEALINGS IN THE SOFTWARE.
*/
import org.broadinstitute.sting.utils.recalibration.covariates.Covariate;
import org.broadinstitute.sting.utils.BaseUtils;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.collections.NestedIntegerArray;
import org.broadinstitute.sting.utils.recalibration.EventType;
import org.broadinstitute.sting.utils.recalibration.ReadCovariates;
import org.broadinstitute.sting.utils.recalibration.RecalibrationTables;
import org.broadinstitute.sting.utils.recalibration.RecalDatum;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.threading.ThreadLocalArray;
import java.util.LinkedList;
import java.util.List;
public class AdvancedRecalibrationEngine extends StandardRecalibrationEngine implements ProtectedPackageSource {
private final static Logger logger = Logger.getLogger(AdvancedRecalibrationEngine.class);
// optimization: only allocate temp arrays once per thread
private final ThreadLocal<byte[]> threadLocalTempQualArray = new ThreadLocalArray<byte[]>(EventType.values().length, byte.class);
private final ThreadLocal<double[]> threadLocalTempFractionalErrorArray = new ThreadLocalArray<double[]>(EventType.values().length, double.class);
public void initialize(final Covariate[] covariates, final RecalibrationTables recalibrationTables) {
super.initialize(covariates, recalibrationTables);
}
final List<NestedIntegerArray<RecalDatum>> allThreadLocalQualityScoreTables = new LinkedList<NestedIntegerArray<RecalDatum>>();
private ThreadLocal<NestedIntegerArray<RecalDatum>> threadLocalQualityScoreTables = new ThreadLocal<NestedIntegerArray<RecalDatum>>() {
@Override
protected synchronized NestedIntegerArray<RecalDatum> initialValue() {
final NestedIntegerArray<RecalDatum> table = recalibrationTables.makeQualityScoreTable();
allThreadLocalQualityScoreTables.add(table);
return table;
}
};
@Override
public void updateDataForRead(final GATKSAMRecord read, final boolean[] skip, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors ) {
public void updateDataForRead( final ReadRecalibrationInfo recalInfo ) {
final GATKSAMRecord read = recalInfo.getRead();
final ReadCovariates readCovariates = recalInfo.getCovariatesValues();
final NestedIntegerArray<RecalDatum> qualityScoreTable = getThreadLocalQualityScoreTable();
for( int offset = 0; offset < read.getReadBases().length; offset++ ) {
if( !skip[offset] ) {
final ReadCovariates readCovariates = covariateKeySetFrom(read);
byte[] tempQualArray = threadLocalTempQualArray.get();
double[] tempFractionalErrorArray = threadLocalTempFractionalErrorArray.get();
tempQualArray[EventType.BASE_SUBSTITUTION.index] = read.getBaseQualities()[offset];
tempFractionalErrorArray[EventType.BASE_SUBSTITUTION.index] = snpErrors[offset];
tempQualArray[EventType.BASE_INSERTION.index] = read.getBaseInsertionQualities()[offset];
tempFractionalErrorArray[EventType.BASE_INSERTION.index] = insertionErrors[offset];
tempQualArray[EventType.BASE_DELETION.index] = read.getBaseDeletionQualities()[offset];
tempFractionalErrorArray[EventType.BASE_DELETION.index] = deletionErrors[offset];
if( ! recalInfo.skip(offset) ) {
for (final EventType eventType : EventType.values()) {
final int[] keys = readCovariates.getKeySet(offset, eventType);
final int eventIndex = eventType.index;
final byte qual = tempQualArray[eventIndex];
final double isError = tempFractionalErrorArray[eventIndex];
final byte qual = recalInfo.getQual(eventType, offset);
final double isError = recalInfo.getErrorFraction(eventType, offset);
combineDatumOrPutIfNecessary(recalibrationTables.getReadGroupTable(), qual, isError, keys[0], eventIndex);
incrementDatumOrPutIfNecessary(recalibrationTables.getQualityScoreTable(), qual, isError, keys[0], keys[1], eventIndex);
incrementDatumOrPutIfNecessary(qualityScoreTable, qual, isError, keys[0], keys[1], eventIndex);
for (int i = 2; i < covariates.length; i++) {
if (keys[i] < 0)
@ -81,4 +76,24 @@ public class AdvancedRecalibrationEngine extends StandardRecalibrationEngine imp
}
}
}
/**
* Get a NestedIntegerArray for a QualityScore table specific to this thread
* @return a non-null NestedIntegerArray ready to be used to collect calibration info for the quality score covariate
*/
private NestedIntegerArray<RecalDatum> getThreadLocalQualityScoreTable() {
return threadLocalQualityScoreTables.get();
}
@Override
public void finalizeData() {
// merge in all of the thread local tables
logger.info("Merging " + allThreadLocalQualityScoreTables.size() + " thread-local quality score tables");
for ( final NestedIntegerArray<RecalDatum> localTable : allThreadLocalQualityScoreTables ) {
recalibrationTables.combineQualityScoreTable(localTable);
}
allThreadLocalQualityScoreTables.clear(); // cleanup after ourselves
super.finalizeData();
}
}

21
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElement.java
View File

@ -39,16 +39,27 @@ public class HeaderElement {
*
* @param location the reference location for the new element
*/
public HeaderElement(int location) {
public HeaderElement(final int location) {
this(new BaseAndQualsCounts(), new BaseAndQualsCounts(), 0, 0, location, new LinkedList<Integer>());
}
/**
* Creates a new HeaderElement with the following default values: - empty consensusBaseCounts - empty
* filteredBaseCounts - empty mappingQuality list
*
* @param location the reference location for the new element
*/
public HeaderElement(final int location, final int insertionsToTheRight) {
this(new BaseAndQualsCounts(), new BaseAndQualsCounts(), insertionsToTheRight, 0, location, new LinkedList<Integer>());
}
/**
* Creates a new HeaderElement with all given parameters
*
* @param consensusBaseCounts the BaseCounts object for the running consensus synthetic read
* @param filteredBaseCounts the BaseCounts object for the filtered data synthetic read
* @param insertionsToTheRight number of insertions to the right of this HeaderElement
* @param nSoftClippedBases number of softclipped bases of this HeaderElement
* @param location the reference location of this reference element
* @param mappingQuality the list of mapping quality values of all reads that contributed to this
* HeaderElement
@ -151,6 +162,14 @@ public class HeaderElement {
throw new ReviewedStingException("Removed too many insertions, header is now negative!");
}
public boolean hasInsertionToTheRight() {
return insertionsToTheRight > 0;
}
public int numInsertionsToTheRight() {
return insertionsToTheRight;
}
/**
* Whether or not the HeaderElement is variant due to excess insertions
*

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
View File

@ -300,7 +300,7 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
// Check if the read goes beyond the boundaries of the chromosome, and hard clip those boundaries.
int chromosomeLength = ref.getGenomeLocParser().getContigInfo(read.getReferenceName()).getSequenceLength();
if (read.getSoftStart() < 0)
read = ReadClipper.hardClipByReadCoordinates(read, 0, -read.getSoftStart() - 1);
read = ReadClipper.hardClipByReadCoordinates(read, 0, -read.getSoftStart());
if (read.getSoftEnd() > chromosomeLength)
read = ReadClipper.hardClipByReadCoordinates(read, chromosomeLength - read.getSoftStart() + 1, read.getReadLength() - 1);

11
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
View File

@ -645,8 +645,15 @@ public class SlidingWindow {
}
}
for (int i = 0; i <= lastStop; i++) // clean up the window header elements up until the end of the variant region. (we keep the last element in case the following element had a read that started with insertion)
windowHeader.remove();
// clean up the window header elements up until the end of the variant region.
// note that we keep the last element of the region in the event that the following element has a read that starts with insertion.
if ( lastStop >= 0 ) {
for (int i = 0; i < lastStop; i++)
windowHeader.remove();
final HeaderElement lastOfRegion = windowHeader.remove();
if ( lastOfRegion.hasInsertionToTheRight() )
windowHeader.addFirst(new HeaderElement(lastOfRegion.getLocation(), lastOfRegion.numInsertionsToTheRight()));
}
}
return allReads;
}

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
View File

@ -8,8 +8,8 @@ import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

6
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java
View File

@ -29,13 +29,13 @@ import net.sf.samtools.SAMUtils;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACcounts;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACset;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.GenotypeLikelihoods;
import java.util.*;

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
View File

@ -31,11 +31,11 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.variant.variantcontext.*;
import java.util.*;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java
View File

@ -8,7 +8,7 @@ import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Allele;
import java.util.*;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
View File

@ -32,7 +32,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.variant.variantcontext.*;
import java.util.*;

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java
View File

@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import net.sf.samtools.SAMUtils;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACset;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@ -11,7 +11,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Allele;
import java.util.ArrayList;
import java.util.Arrays;

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java
View File

@ -31,7 +31,8 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.variantcontext.*;
import java.util.*;

8
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java
View File

@ -10,10 +10,10 @@ import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.SimpleTimer;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
import java.io.*;
import java.util.*;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java
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@ -4,7 +4,7 @@ import org.apache.commons.lang.ArrayUtils;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.variant.variantcontext.*;
import java.util.ArrayList;
import java.util.Arrays;

9
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
View File

@ -27,9 +27,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
import org.broadinstitute.sting.gatk.walkers.genotyper.GeneralPloidyGenotypeLikelihoods;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.variant.variantcontext.*;
import java.util.*;
@ -532,7 +533,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
}
// if there is no mass on the (new) likelihoods, then just no-call the sample
if ( MathUtils.sum(newLikelihoods) > VariantContextUtils.SUM_GL_THRESH_NOCALL ) {
if ( MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL ) {
newGTs.add(GenotypeBuilder.create(g.getSampleName(), NO_CALL_ALLELES));
}
else {
@ -544,7 +545,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
gb.PL(newLikelihoods);
// if we weren't asked to assign a genotype, then just no-call the sample
if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > VariantContextUtils.SUM_GL_THRESH_NOCALL )
if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL )
gb.alleles(NO_CALL_ALLELES);
else
assignGenotype(gb, newLikelihoods, allelesToUse, ploidy);

23
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
View File

@ -36,7 +36,9 @@ import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.variantcontext.*;
import java.io.PrintStream;
import java.util.*;
@ -44,13 +46,15 @@ import java.util.*;
public class GenotypingEngine {
private final boolean DEBUG;
private final boolean USE_FILTERED_READ_MAP_FOR_ANNOTATIONS;
private final static List<Allele> noCall = new ArrayList<Allele>(); // used to noCall all genotypes until the exact model is applied
private final static Allele SYMBOLIC_UNASSEMBLED_EVENT_ALLELE = Allele.create("<UNASSEMBLED_EVENT>", false);
private final VariantAnnotatorEngine annotationEngine;
public GenotypingEngine( final boolean DEBUG, final VariantAnnotatorEngine annotationEngine ) {
public GenotypingEngine( final boolean DEBUG, final VariantAnnotatorEngine annotationEngine, final boolean USE_FILTERED_READ_MAP_FOR_ANNOTATIONS ) {
this.DEBUG = DEBUG;
this.annotationEngine = annotationEngine;
this.USE_FILTERED_READ_MAP_FOR_ANNOTATIONS = USE_FILTERED_READ_MAP_FOR_ANNOTATIONS;
noCall.add(Allele.NO_CALL);
}
@ -156,7 +160,7 @@ public class GenotypingEngine {
}
// Merge the event to find a common reference representation
final VariantContext mergedVC = VariantContextUtils.simpleMerge(genomeLocParser, eventsAtThisLoc, priorityList, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, null, false, false);
final VariantContext mergedVC = VariantContextUtils.simpleMerge(eventsAtThisLoc, priorityList, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, null, false, false);
if( mergedVC == null ) { continue; }
// let's update the Allele keys in the mapper because they can change after merging when there are complex events
@ -192,11 +196,13 @@ public class GenotypingEngine {
}
final VariantContext call = UG_engine.calculateGenotypes(new VariantContextBuilder(mergedVC).genotypes(genotypes).make(), UG_engine.getUAC().GLmodel);
if( call != null ) {
final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = filterToOnlyOverlappingReads( genomeLocParser, alleleReadMap, perSampleFilteredReadList, call );
final Map<String, PerReadAlleleLikelihoodMap> alleleReadMap_annotations = ( USE_FILTERED_READ_MAP_FOR_ANNOTATIONS ? alleleReadMap :
convertHaplotypeReadMapToAlleleReadMap( haplotypeReadMap, alleleMapper, 0.0, UG_engine.getUAC().contaminationLog ) );
final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = filterToOnlyOverlappingReads( genomeLocParser, alleleReadMap_annotations, perSampleFilteredReadList, call );
VariantContext annotatedCall = annotationEngine.annotateContext(stratifiedReadMap, call);
if( annotatedCall.getAlleles().size() != mergedVC.getAlleles().size() ) { // some alleles were removed so reverseTrimming might be necessary!
annotatedCall = VariantContextUtils.reverseTrimAlleles(annotatedCall);
annotatedCall = GATKVariantContextUtils.reverseTrimAlleles(annotatedCall);
}
returnCalls.add( annotatedCall );
@ -339,12 +345,7 @@ public class GenotypingEngine {
}
// count up the co-occurrences of the events for the R^2 calculation
for( final String sample : samples ) {
final HashSet<String> sampleSet = new HashSet<String>(1);
sampleSet.add(sample);
final List<Allele> alleleList = new ArrayList<Allele>();
alleleList.add(Allele.create(h.getBases()));
final double haplotypeLikelihood = LikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods( sampleSet, haplotypeReadMap, alleleList )[0][0];
final double haplotypeLikelihood = LikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods( Collections.singleton(sample), haplotypeReadMap, Collections.singletonList(Allele.create(h.getBases())) )[0][0];
if( thisHapVC == null ) {
if( nextHapVC == null ) { x11 = MathUtils.approximateLog10SumLog10(x11, haplotypeLikelihood); }
else { x12 = MathUtils.approximateLog10SumLog10(x12, haplotypeLikelihood); }

26
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
View File

@ -48,8 +48,8 @@ import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState;
import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.fragments.FragmentCollection;
@ -61,8 +61,8 @@ import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.variantcontext.*;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import java.io.FileNotFoundException;
import java.io.PrintStream;
@ -130,18 +130,26 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
protected String keepRG = null;
@Argument(fullName="minPruning", shortName="minPruning", doc = "The minimum allowed pruning factor in assembly graph. Paths with <= X supporting kmers are pruned from the graph", required = false)
protected int MIN_PRUNE_FACTOR = 1;
protected int MIN_PRUNE_FACTOR = 2;
@Advanced
@Argument(fullName="gcpHMM", shortName="gcpHMM", doc="Flat gap continuation penalty for use in the Pair HMM", required = false)
protected int gcpHMM = 10;
@Advanced
@Argument(fullName="minKmer", shortName="minKmer", doc="Minimum kmer length to use in the assembly graph", required = false)
protected int minKmer = 11;
@Argument(fullName="downsampleRegion", shortName="dr", doc="coverage, per-sample, to downsample each active region to", required = false)
protected int DOWNSAMPLE_PER_SAMPLE_PER_REGION = 1000;
@Argument(fullName="useAllelesTrigger", shortName="allelesTrigger", doc = "If specified, use additional trigger on variants found in an external alleles file", required=false)
protected boolean USE_ALLELES_TRIGGER = false;
@Advanced
@Argument(fullName="useFilteredReadsForAnnotations", shortName="useFilteredReadsForAnnotations", doc = "If specified, use the contamination-filtered read maps for the purposes of annotating variants", required=false)
protected boolean USE_FILTERED_READ_MAP_FOR_ANNOTATIONS = false;
/**
* rsIDs from this file are used to populate the ID column of the output. Also, the DB INFO flag will be set when appropriate.
* dbSNP is not used in any way for the calculations themselves.
@ -234,7 +242,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
samplesList.addAll( samples );
// initialize the UnifiedGenotyper Engine which is used to call into the exact model
final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection( SCAC ); // this adapter is used so that the full set of unused UG arguments aren't exposed to the HC user
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY);
// create a UAC but with the exactCallsLog = null, so we only output the log for the HC caller itself, if requested
UnifiedArgumentCollection simpleUAC = new UnifiedArgumentCollection(UAC);
@ -244,7 +252,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
simpleUAC.STANDARD_CONFIDENCE_FOR_EMITTING = Math.min( 4.0, UAC.STANDARD_CONFIDENCE_FOR_EMITTING ); // low values used for isActive determination only, default/user-specified values used for actual calling
simpleUAC.CONTAMINATION_FRACTION = 0.0;
simpleUAC.exactCallsLog = null;
UG_engine_simple_genotyper = new UnifiedGenotyperEngine(getToolkit(), simpleUAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
UG_engine_simple_genotyper = new UnifiedGenotyperEngine(getToolkit(), simpleUAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY);
// initialize the output VCF header
final VariantAnnotatorEngine annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());
@ -278,9 +286,9 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
throw new UserException.CouldNotReadInputFile(getToolkit().getArguments().referenceFile, e);
}
assemblyEngine = new SimpleDeBruijnAssembler( DEBUG, graphWriter );
assemblyEngine = new SimpleDeBruijnAssembler( DEBUG, graphWriter, minKmer );
likelihoodCalculationEngine = new LikelihoodCalculationEngine( (byte)gcpHMM, DEBUG, pairHMM );
genotypingEngine = new GenotypingEngine( DEBUG, annotationEngine );
genotypingEngine = new GenotypingEngine( DEBUG, annotationEngine, USE_FILTERED_READ_MAP_FOR_ANNOTATIONS );
}
//---------------------------------------------------------------------------------------------------------------

20
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java
View File

@ -39,18 +39,18 @@ import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.SWPairwiseAlignment;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
import org.broadinstitute.variant.variantcontext.VariantContextUtils;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
import java.util.*;

5
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
View File

@ -29,16 +29,13 @@ import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pairhmm.*;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Allele;
import java.io.PrintStream;
import java.util.*;
public class LikelihoodCalculationEngine {

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java
View File

@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.ArrayList;

15
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java
View File

@ -11,8 +11,8 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.jgrapht.graph.DefaultDirectedGraph;
import java.io.PrintStream;
@ -28,7 +28,7 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
private static final int KMER_OVERLAP = 5; // the additional size of a valid chunk of sequence, used to string together k-mers
private static final int NUM_BEST_PATHS_PER_KMER_GRAPH = 11;
private static final byte MIN_QUALITY = (byte) 17;
private static final byte MIN_QUALITY = (byte) 16;
// Smith-Waterman parameters originally copied from IndelRealigner
private static final double SW_MATCH = 5.0; // 1.0;
@ -39,13 +39,15 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
private final boolean DEBUG;
private final PrintStream GRAPH_WRITER;
private final ArrayList<DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge>> graphs = new ArrayList<DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge>>();
private final int MIN_KMER;
private int PRUNE_FACTOR = 1;
private int PRUNE_FACTOR = 2;
public SimpleDeBruijnAssembler( final boolean debug, final PrintStream graphWriter ) {
public SimpleDeBruijnAssembler( final boolean debug, final PrintStream graphWriter, final int minKmer ) {
super();
DEBUG = debug;
GRAPH_WRITER = graphWriter;
MIN_KMER = minKmer;
}
public ArrayList<Haplotype> runLocalAssembly( final ActiveRegion activeRegion, final Haplotype refHaplotype, final byte[] fullReferenceWithPadding, final GenomeLoc refLoc, final int PRUNE_FACTOR, final ArrayList<VariantContext> activeAllelesToGenotype ) {
@ -72,8 +74,9 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
protected void createDeBruijnGraphs( final List<GATKSAMRecord> reads, final Haplotype refHaplotype ) {
graphs.clear();
final int maxKmer = refHaplotype.getBases().length;
// create the graph
for( int kmer = 31; kmer <= 75; kmer += 6 ) {
for( int kmer = MIN_KMER; kmer <= maxKmer; kmer += 6 ) {
final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph = new DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge>(DeBruijnEdge.class);
if( createGraphFromSequences( graph, reads, kmer, refHaplotype, DEBUG ) ) {
graphs.add(graph);

2
protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java
View File

@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.downsampling.AlleleBiasedDownsamplingUtils;
import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Allele;
import java.io.PrintStream;
import java.util.*;

37
protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
View File

@ -38,7 +38,8 @@ public class BQSRIntegrationTest extends WalkerTest {
args +
" -knownSites " + (reference.equals(b36KGReference) ? b36dbSNP129 : hg18dbSNP132) +
" --allow_potentially_misencoded_quality_scores" + // TODO -- remove me when we get new SOLiD bams
" -o %s";
" -o %s" +
" -sortAllCols";
}
@Override
@ -52,21 +53,21 @@ public class BQSRIntegrationTest extends WalkerTest {
String HiSeqBam = privateTestDir + "HiSeq.1mb.1RG.bam";
String HiSeqInterval = "chr1:10,000,000-10,100,000";
return new Object[][]{
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, "", "4fd3c9ad97e6ac58cba644a76564c9f7")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov ContextCovariate", "2620f734cce20f70ce13afd880e46e5c")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov CycleCovariate", "5eb3b94e767da19a4c037ee132e4b19a")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --indels_context_size 4", "ab261d291b107a3da7897759c0e4fa89")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "292303f649fbb19dc05d4a0197a49eeb")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "8ced9d1094493f17fb1876b818a64541")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "abb838131e403d39820dbd66932d1ed0")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", "", "f70d8b5358bc2f76696f14b7a807ede0")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-10,200,000", "", "4c0f63e06830681560a1e9f9aad9fe98")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.1RG.bam", "1:10,000,000-10,200,000", "", "8f62aa0e75770204c98d8299793cc53c")},
{new BQSRTest(b36KGReference, validationDataLocation + "originalQuals.1kg.chr1.1-1K.1RG.bam", "1:1-1,000", " -OQ", "03c29a0c1d21f72b12daf51cec111599")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-20,000,000", " --solid_recal_mode REMOVE_REF_BIAS", "7080b2cad02ec6e67ebc766b2dccebf8")},
{new BQSRTest(b36KGReference, privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam", "1:50,000-80,000", " --solid_nocall_strategy LEAVE_READ_UNRECALIBRATED", "30e76055c16843b6e33e5b9bd8ced57c")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:anyNameABCD,VCF " + privateTestDir + "vcfexample3.vcf", "f70d8b5358bc2f76696f14b7a807ede0")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:bed " + validationDataLocation + "bqsrKnownTest.bed", "5e657fd6a44dcdc7674b6e5a2de5dc83")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, "", "2f250fecb930e0dfe0f63fe0fed3960b")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov ContextCovariate", "26c8d7226139a040557b1d3b1c8792f0")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov CycleCovariate", "9b43a1839cb6ea03aec1d96f15ca8efb")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --indels_context_size 4", "3159a9d136c45e4a65d46a23dc8fd3b5")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "bb7262829effbbdbc8d88dd36f480368")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "fbb002fa2b9197c4b555852dccc11562")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "7392acb71131a60a527ca32715fc59be")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", "", "49d4383896a90795d94138db1410a7df")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-10,200,000", "", "427448eff98cf194cc7217c0b1401e79")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.1RG.bam", "1:10,000,000-10,200,000", "", "50cd1a10b6ecb3d09f90f1e4a66da95d")},
{new BQSRTest(b36KGReference, validationDataLocation + "originalQuals.1kg.chr1.1-1K.1RG.bam", "1:1-1,000", " -OQ", "1dc71561c9d0fb56f9876cb5043c5376")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-20,000,000", " --solid_recal_mode REMOVE_REF_BIAS", "13e8f032e76340b114847c90af0a1f8a")},
{new BQSRTest(b36KGReference, privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam", "1:50,000-80,000", " --solid_nocall_strategy LEAVE_READ_UNRECALIBRATED", "03f58ae4f9d203034e895a3636fc108f")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:anyNameABCD,VCF " + privateTestDir + "vcfexample3.vcf", "49d4383896a90795d94138db1410a7df")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:bed " + validationDataLocation + "bqsrKnownTest.bed", "2db2ef8c2d63e167663d70340182f49a")},
};
}
@ -100,6 +101,7 @@ public class BQSRIntegrationTest extends WalkerTest {
" -knownSites " + b36dbSNP129 +
" -L 1:10,000,000-10,200,000" +
" -o /dev/null" +
" -sortAllCols" +
" --plot_pdf_file /dev/null" +
" --intermediate_csv_file %s",
Arrays.asList("d1c38a3418979400630e2bca1140689c"));
@ -114,7 +116,8 @@ public class BQSRIntegrationTest extends WalkerTest {
" -I " + privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam" +
" -L 1:50,000-80,000" +
" --allow_potentially_misencoded_quality_scores" + // TODO -- remove me when we get new SOLiD bams
" -o %s",
" -o %s" +
" -sortAllCols",
1, // just one output file
UserException.class);
executeTest("testBQSRFailWithSolidNoCall", spec);

18
protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
View File

@ -17,6 +17,8 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
final String COREDUCTION_BAM_A = validationDataLocation + "coreduction.test.A.bam";
final String COREDUCTION_BAM_B = validationDataLocation + "coreduction.test.B.bam";
final String COREDUCTION_L = " -L 1:1,853,860-1,854,354 -L 1:1,884,131-1,892,057";
final String OFFCONTIG_BAM = privateTestDir + "readOffb37contigMT.bam";
final String INSERTIONS_AT_EDGE_OF_CONSENSUS_BAM = privateTestDir + "rr-too-many-insertions.bam";
private void RRTest(String testName, String args, String md5) {
String base = String.format("-T ReduceReads -npt -R %s -I %s ", REF, BAM) + " -o %s ";
@ -29,6 +31,12 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
RRTest("testDefaultCompression ", L, "98080d3c53f441564796fc143cf510da");
}
@Test(enabled = true)
public void testInsertionsAtEdgeOfConsensus() {
String base = String.format("-T ReduceReads -npt -R %s -I %s ", REF, INSERTIONS_AT_EDGE_OF_CONSENSUS_BAM) + " -o %s ";
executeTest("testInsertionsAtEdgeOfConsensus", new WalkerTestSpec(base, Arrays.asList("2a6e08a0206bd8ec7671224c4a55dae0")));
}
@Test(enabled = true)
public void testMultipleIntervals() {
String intervals = "-L 20:10,100,000-10,100,500 -L 20:10,200,000-10,200,500 -L 20:10,300,000-10,300,500 -L 20:10,400,000-10,500,000 -L 20:10,500,050-10,500,060 -L 20:10,600,000-10,600,015 -L 20:10,700,000-10,700,110";
@ -86,5 +94,15 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
executeTest("testCoReduction", new WalkerTestSpec(base, Arrays.asList("5c30fde961a1357bf72c15144c01981b")));
}
/**
* Bug happens when reads are soft-clipped off the contig (usually in the MT). This test guarantees no changes to the upstream code will
* break the current hard-clipping routine that protects reduce reads from such reads.
*/
@Test(enabled = true)
public void testReadOffContig() {
String base = String.format("-T ReduceReads -npt -R %s -I %s ", REF, OFFCONTIG_BAM) + " -o %s ";
executeTest("testReadOffContig", new WalkerTestSpec(base, Arrays.asList("2f17c1a78e9d0138217fdb83cede8f68")));
}
}

4
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java
View File

@ -28,11 +28,11 @@ import net.sf.samtools.SAMUtils;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.variant.variantcontext.*;
import org.testng.Assert;
import org.testng.annotations.Test;

4
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
View File

@ -70,12 +70,12 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","481452ad7d6378cffb5cd834cc621d55");
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","6987b89e04dcb604d3743bb09aa9587d");
}
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","812957e51277aca9925c1a7bb4d9a118");
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","d0780f70365ed1b431099fd3b4cec449");
}
@Test(enabled = true)

16
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() {
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,
Arrays.asList("97df6c2a8d390d43b9bdf56c979d9b09"));
Arrays.asList("b41b95aaa2c453c9b75b3b29a9c2718e"));
executeTest("test Multiple SNP alleles", spec);
}
@ -96,7 +96,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
//
// --------------------------------------------------------------------------------------------------------------
private final static String COMPRESSED_OUTPUT_MD5 = "3eba6c309514d1e9ee06a20a112b68e6";
private final static String COMPRESSED_OUTPUT_MD5 = "af8187e2baf516dde1cddea787a52b8a";
@Test
public void testCompressedOutput() {
@ -289,7 +289,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("50329e15e5139be9e3b643f0b3ba8a53"));
Arrays.asList("f6f8fbf733f20fbc1dd9ebaf8faefe6c"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@ -304,7 +304,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -minIndelCnt 1" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("2b85e3bd6bf981afaf7324666740d74b"));
Arrays.asList("4438ad0f03bbdd182d9bb59b15af0fa5"));
executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
}
@ -317,7 +317,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("a6fd46eff78827060451a62cffd698a7"));
Arrays.asList("27b4ace2ad5a83d8cccb040f97f29183"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
@ -345,13 +345,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSampleIndels1() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
Arrays.asList("69df7a00f800204564ca3726e1871132"));
Arrays.asList("d3d518448b01bf0f751824b3d946cd04"));
List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
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,
Arrays.asList("1256a7eceff2c2374c231ff981df486d"));
Arrays.asList("2ea18a3e8480718a80a415d3fea79f54"));
executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
}
@ -462,7 +462,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testReducedBamINDELs() {
testReducedCalling("INDEL", "3c02ee5187933bed44dc416a2e28511f");
testReducedCalling("INDEL", "9d5418ddf1b227ae4d463995507f2b1c");
}

4
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java
View File

@ -4,8 +4,8 @@ import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java
View File

@ -4,7 +4,7 @@ import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Allele;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java
View File

@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.variant.variantcontext.*;
import org.testng.Assert;
import org.testng.annotations.BeforeSuite;
import org.testng.annotations.DataProvider;

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

@ -2,10 +2,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.walkers.genotyper.GeneralPloidyGenotypeLikelihoods;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.testng.Assert;
import org.testng.annotations.BeforeSuite;
import org.testng.annotations.DataProvider;

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

@ -3,10 +3,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

6
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java
View File

@ -10,9 +10,9 @@ import net.sf.picard.reference.ReferenceSequenceFile;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;

20
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -21,30 +21,30 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "d602d40852ad6d2d094be07e60cf95bd");
HCTest(CEUTRIO_BAM, "", "839de31b41d4186e2b12a5601525e894");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "70ad9d53dda4d302b879ca2b7dd5b368");
HCTest(NA12878_BAM, "", "2b68faa0e0493d92491d74b8f731963a");
}
// TODO -- add more tests for GGA mode, especially with input alleles that are complex variants and/or not trimmed
@Test
public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
"fe84caa79f59ecbd98fcbcd5b30ab164");
"a2d56179cd19a41f8bfb995e225320bb");
}
private void HCTestComplexVariants(String bam, String args, String md5) {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, bam) + " -L 20:10028767-10028967 -L 20:10431524-10431924 -L 20:10723661-10724061 -L 20:10903555-10903955 --no_cmdline_in_header -o %s -minPruning 2";
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, bam) + " -L 20:10028767-10028967 -L 20:10431524-10431924 -L 20:10723661-10724061 -L 20:10903555-10903955 --no_cmdline_in_header -o %s -minPruning 4";
final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
executeTest("testHaplotypeCallerComplexVariants: args=" + args, spec);
}
@Test
public void testHaplotypeCallerMultiSampleComplex() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "883871f8bb4099f69fd804f8a6181954");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "fd8d2ae8db9d98e932b0a7f345631eec");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -55,7 +55,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleSymbolic() {
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "338ab3b7dc3d54df8af94c0811028a75");
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "0761ff5cbf279be467833fa6708bf360");
}
private void HCTestIndelQualityScores(String bam, String args, String md5) {
@ -66,20 +66,20 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "aff11b014ca42bfa301bcced5f5e54dd");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "6380e25c1ec79c6ae2f891ced15bf4e1");
}
@Test
public void HCTestProblematicReadsModifiedInActiveRegions() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("2f4ed6dc969bee041215944a9b24328f"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("3a096d6139d15dcab82f5b091d08489d"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
}
@Test
public void HCTestStructuralIndels() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("d8d6f2ebe79bca81c8a0911daa153b89"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("a518c7436544f2b5f71c9d9427ce1cce"));
executeTest("HCTestStructuralIndels: ", spec);
}
@ -93,7 +93,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
Arrays.asList("d01cb5f77ed5aca1d228cfbce9364c21"));
Arrays.asList("8a400b0c46f41447fcc35a907e34f384"));
executeTest("HC calling on a ReducedRead BAM", spec);
}
}

43
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssemblerUnitTest.java
View File

@ -10,16 +10,11 @@ import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.walkers.genotyper.ArtificialReadPileupTestProvider;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.jgrapht.graph.DefaultDirectedGraph;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.PrintStream;
import java.util.*;
@ -146,44 +141,6 @@ public class SimpleDeBruijnAssemblerUnitTest extends BaseTest {
Assert.assertTrue(graphEquals(graph, expectedGraph));
}
@Test(enabled=false)
// not ready yet
public void testBasicGraphCreation() {
final ArtificialReadPileupTestProvider refPileupTestProvider = new ArtificialReadPileupTestProvider(1,"ref");
final byte refBase = refPileupTestProvider.getReferenceContext().getBase();
final String altBase = (refBase==(byte)'A'?"C":"A");
final int matches = 50;
final int mismatches = 50;
Map<String,AlignmentContext> refContext = refPileupTestProvider.getAlignmentContextFromAlleles(0, altBase, new int[]{matches, mismatches}, false, 30);
PrintStream graphWriter = null;
try{
graphWriter = new PrintStream("du.txt");
} catch (Exception e) {}
SimpleDeBruijnAssembler assembler = new SimpleDeBruijnAssembler(true,graphWriter);
final Haplotype refHaplotype = new Haplotype(refPileupTestProvider.getReferenceContext().getBases());
refHaplotype.setIsReference(true);
assembler.createDeBruijnGraphs(refContext.get(refPileupTestProvider.getSampleNames().get(0)).getBasePileup().getReads(), refHaplotype);
/* // clean up the graphs by pruning and merging
for( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph : graphs ) {
SimpleDeBruijnAssembler.pruneGraph( graph, PRUNE_FACTOR );
//eliminateNonRefPaths( graph );
SimpleDeBruijnAssembler.mergeNodes( graph );
}
*/
if( graphWriter != null ) {
assembler.printGraphs();
}
int k=2;
// find the best paths in the graphs
// return findBestPaths( refHaplotype, fullReferenceWithPadding, refLoc, activeAllelesToGenotype, activeRegion.getExtendedLoc() );
}
@Test(enabled = true)
public void testEliminateNonRefPaths() {
DefaultDirectedGraph<DeBruijnVertex,DeBruijnEdge> graph = new DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge>(DeBruijnEdge.class);

2
protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java
View File

@ -29,7 +29,7 @@ package org.broadinstitute.sting.utils.pairhmm;
// the imports for unit testing.
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils;
import org.testng.Assert;
import org.testng.annotations.DataProvider;

2
public/java/src/org/broadinstitute/sting/alignment/Alignment.java
View File

@ -1,7 +1,7 @@
package org.broadinstitute.sting.alignment;
import net.sf.samtools.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;

2
public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java
View File

@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;

2
public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
View File

@ -4,7 +4,7 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.samtools.*;
import org.broadinstitute.sting.alignment.Aligner;
import org.broadinstitute.sting.alignment.Alignment;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.File;

2
public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java
View File

@ -6,7 +6,7 @@ import org.broadinstitute.sting.alignment.Alignment;
import org.broadinstitute.sting.alignment.bwa.BWAAligner;
import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
import org.broadinstitute.sting.alignment.reference.bwt.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils;
import java.io.File;

2
public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java
View File

@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.arguments;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
/**
* @author ebanks

2
public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
View File

@ -4,7 +4,7 @@ import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.io.File;
import java.io.PrintStream;

2
public/java/src/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java
View File

@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.arguments;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
/**
* @author ebanks

2
public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
View File

@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.contexts;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;

51
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
View File

@ -23,17 +23,17 @@
*/
package org.broadinstitute.sting.gatk.datasources.reads;
import org.broad.tribble.util.SeekableBufferedStream;
import org.broad.tribble.util.SeekableFileStream;
import net.sf.samtools.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.*;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import java.nio.channels.FileChannel;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
@ -68,6 +68,9 @@ public class GATKBAMIndex {
private final File mFile;
//TODO: figure out a good value for this buffer size
private final int BUFFERED_STREAM_BUFFER_SIZE=8192;
/**
* Number of sequences stored in this index.
*/
@ -78,8 +81,8 @@ public class GATKBAMIndex {
*/
private final long[] sequenceStartCache;
private FileInputStream fileStream;
private FileChannel fileChannel;
private SeekableFileStream fileStream;
private SeekableBufferedStream bufferedStream;
public GATKBAMIndex(final File file) {
mFile = file;
@ -277,7 +280,6 @@ public class GATKBAMIndex {
for (int i = sequenceIndex; i < referenceSequence; i++) {
sequenceStartCache[i] = position();
// System.out.println("# Sequence TID: " + i);
final int nBins = readInteger();
// System.out.println("# nBins: " + nBins);
@ -290,15 +292,18 @@ public class GATKBAMIndex {
final int nLinearBins = readInteger();
// System.out.println("# nLinearBins: " + nLinearBins);
skipBytes(8 * nLinearBins);
}
sequenceStartCache[referenceSequence] = position();
}
private void openIndexFile() {
try {
fileStream = new FileInputStream(mFile);
fileChannel = fileStream.getChannel();
fileStream = new SeekableFileStream(mFile);
bufferedStream = new SeekableBufferedStream(fileStream,BUFFERED_STREAM_BUFFER_SIZE);
}
catch (IOException exc) {
throw new ReviewedStingException("Unable to open index file (" + exc.getMessage() +")" + mFile, exc);
@ -307,7 +312,7 @@ public class GATKBAMIndex {
private void closeIndexFile() {
try {
fileChannel.close();
bufferedStream.close();
fileStream.close();
}
catch (IOException exc) {
@ -352,7 +357,12 @@ public class GATKBAMIndex {
private void read(final ByteBuffer buffer) {
try {
int bytesExpected = buffer.limit();
int bytesRead = fileChannel.read(buffer);
//BufferedInputStream cannot read directly into a byte buffer, so we read into an array
//and put the result into the bytebuffer after the if statement.
//SeekableBufferedStream is evil, it will "read" beyond the end of the file if you let it!
final int bytesToRead = (int) Math.min(bufferedStream.length() - bufferedStream.position(), bytesExpected); //min of int and long will definitely be castable to an int.
int bytesRead = bufferedStream.read(byteArray,0,bytesToRead);
// We have a rigid expectation here to read in exactly the number of bytes we've limited
// our buffer to -- if we read in fewer bytes than this, or encounter EOF (-1), the index
@ -363,6 +373,7 @@ public class GATKBAMIndex {
"Please try re-indexing the corresponding BAM file.",
mFile));
}
buffer.put(byteArray,0,bytesRead);
}
catch(IOException ex) {
throw new ReviewedStingException("Index: unable to read bytes from index file " + mFile);
@ -376,10 +387,13 @@ public class GATKBAMIndex {
*/
private ByteBuffer buffer = null;
//BufferedStream don't read into ByteBuffers, so we need this temporary array
private byte[] byteArray=null;
private ByteBuffer getBuffer(final int size) {
if(buffer == null || buffer.capacity() < size) {
// Allocate a new byte buffer. For now, make it indirect to make sure it winds up on the heap for easier debugging.
buffer = ByteBuffer.allocate(size);
byteArray = new byte[size];
buffer.order(ByteOrder.LITTLE_ENDIAN);
}
buffer.clear();
@ -389,7 +403,13 @@ public class GATKBAMIndex {
private void skipBytes(final int count) {
try {
fileChannel.position(fileChannel.position() + count);
//try to skip forward the requested amount.
long skipped = bufferedStream.skip(count);
if( skipped != count ) { //if not managed to skip the requested amount
throw new ReviewedStingException("Index: unable to reposition file channel of index file " + mFile);
}
}
catch(IOException ex) {
throw new ReviewedStingException("Index: unable to reposition file channel of index file " + mFile);
@ -398,7 +418,8 @@ public class GATKBAMIndex {
private void seek(final long position) {
try {
fileChannel.position(position);
//to seek a new position, move the fileChannel, and reposition the bufferedStream
bufferedStream.seek(position);
}
catch(IOException ex) {
throw new ReviewedStingException("Index: unable to reposition of file channel of index file " + mFile);
@ -411,7 +432,7 @@ public class GATKBAMIndex {
*/
private long position() {
try {
return fileChannel.position();
return bufferedStream.position();
}
catch (IOException exc) {
throw new ReviewedStingException("Unable to read position from index file " + mFile, exc);

17
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
View File

@ -44,6 +44,7 @@ import org.broadinstitute.sting.utils.SimpleTimer;
import org.broadinstitute.sting.utils.baq.ReadTransformingIterator;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
import org.broadinstitute.sting.utils.sam.GATKSamRecordFactory;
import java.io.File;
@ -252,9 +253,10 @@ public class SAMDataSource {
if(readBufferSize != null)
ReadShard.setReadBufferSize(readBufferSize); // TODO: use of non-final static variable here is just awful, especially for parallel tests
else {
// Choose a sensible default for the read buffer size. For the moment, we're picking 1000 reads per BAM per shard (which effectively
// will mean per-thread once ReadWalkers are parallelized) with a max cap of 250K reads in memory at once.
ReadShard.setReadBufferSize(Math.min(10000*samFiles.size(),250000));
// Choose a sensible default for the read buffer size.
// Previously we we're picked 100000 reads per BAM per shard with a max cap of 250K reads in memory at once.
// Now we are simply setting it to 100K reads
ReadShard.setReadBufferSize(100000);
}
resourcePool = new SAMResourcePool(Integer.MAX_VALUE);
@ -894,9 +896,11 @@ public class SAMDataSource {
long lastTick = timer.currentTime();
for(final SAMReaderID readerID: readerIDs) {
final ReaderInitializer init = new ReaderInitializer(readerID).call();
if (removeProgramRecords) {
init.reader.getFileHeader().setProgramRecords(new ArrayList<SAMProgramRecord>());
}
if (threadAllocation.getNumIOThreads() > 0) {
inputStreams.put(init.readerID, init.blockInputStream); // get from initializer
}
@ -916,6 +920,13 @@ public class SAMDataSource {
for(SAMFileReader reader: readers.values())
headers.add(reader.getFileHeader());
headerMerger = new SamFileHeaderMerger(SAMFileHeader.SortOrder.coordinate,headers,true);
// update all read groups to GATKSAMRecordReadGroups
final List<SAMReadGroupRecord> gatkReadGroups = new LinkedList<SAMReadGroupRecord>();
for ( final SAMReadGroupRecord rg : headerMerger.getMergedHeader().getReadGroups() ) {
gatkReadGroups.add(new GATKSAMReadGroupRecord(rg));
}
headerMerger.getMergedHeader().setReadGroups(gatkReadGroups);
}
final private void printReaderPerformance(final int nExecutedTotal,

104
public/java/src/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIterator.java
View File

@ -104,6 +104,56 @@ public class PerSampleDownsamplingReadsIterator implements StingSAMIterator {
readComparator.compare(orderedDownsampledReadsCache.peek(), earliestPendingRead) <= 0;
}
private boolean fillDownsampledReadsCache() {
SAMRecord prevRead = null;
int numPositionalChanges = 0;
// Continue submitting reads to the per-sample downsamplers until the read at the top of the priority queue
// can be released without violating global sort order
while ( nestedSAMIterator.hasNext() && ! readyToReleaseReads() ) {
SAMRecord read = nestedSAMIterator.next();
String sampleName = read.getReadGroup() != null ? read.getReadGroup().getSample() : null;
ReadsDownsampler<SAMRecord> thisSampleDownsampler = perSampleDownsamplers.get(sampleName);
if ( thisSampleDownsampler == null ) {
thisSampleDownsampler = downsamplerFactory.newInstance();
perSampleDownsamplers.put(sampleName, thisSampleDownsampler);
}
thisSampleDownsampler.submit(read);
processFinalizedAndPendingItems(thisSampleDownsampler);
if ( prevRead != null && prevRead.getAlignmentStart() != read.getAlignmentStart() ) {
numPositionalChanges++;
}
// Periodically inform all downsamplers of the current position in the read stream. This is
// to prevent downsamplers for samples with sparser reads than others from getting stuck too
// long in a pending state.
if ( numPositionalChanges > 0 && numPositionalChanges % DOWNSAMPLER_POSITIONAL_UPDATE_INTERVAL == 0 ) {
for ( ReadsDownsampler<SAMRecord> perSampleDownsampler : perSampleDownsamplers.values() ) {
perSampleDownsampler.signalNoMoreReadsBefore(read);
processFinalizedAndPendingItems(perSampleDownsampler);
}
}
prevRead = read;
}
if ( ! nestedSAMIterator.hasNext() ) {
for ( ReadsDownsampler<SAMRecord> perSampleDownsampler : perSampleDownsamplers.values() ) {
perSampleDownsampler.signalEndOfInput();
if ( perSampleDownsampler.hasFinalizedItems() ) {
orderedDownsampledReadsCache.addAll(perSampleDownsampler.consumeFinalizedItems());
}
}
earliestPendingRead = null;
earliestPendingDownsampler = null;
}
return readyToReleaseReads();
}
private void updateEarliestPendingRead( ReadsDownsampler<SAMRecord> currentDownsampler ) {
// If there is no recorded earliest pending read and this downsampler has pending items,
// then this downsampler's first pending item becomes the new earliest pending read:
@ -135,57 +185,11 @@ public class PerSampleDownsamplingReadsIterator implements StingSAMIterator {
}
}
private boolean fillDownsampledReadsCache() {
SAMRecord prevRead = null;
int numPositionalChanges = 0;
// Continue submitting reads to the per-sample downsamplers until the read at the top of the priority queue
// can be released without violating global sort order
while ( nestedSAMIterator.hasNext() && ! readyToReleaseReads() ) {
SAMRecord read = nestedSAMIterator.next();
String sampleName = read.getReadGroup() != null ? read.getReadGroup().getSample() : null;
ReadsDownsampler<SAMRecord> thisSampleDownsampler = perSampleDownsamplers.get(sampleName);
if ( thisSampleDownsampler == null ) {
thisSampleDownsampler = downsamplerFactory.newInstance();
perSampleDownsamplers.put(sampleName, thisSampleDownsampler);
}
thisSampleDownsampler.submit(read);
updateEarliestPendingRead(thisSampleDownsampler);
if ( prevRead != null && prevRead.getAlignmentStart() != read.getAlignmentStart() ) {
numPositionalChanges++;
}
// Periodically inform all downsamplers of the current position in the read stream. This is
// to prevent downsamplers for samples with sparser reads than others from getting stuck too
// long in a pending state.
if ( numPositionalChanges > 0 && numPositionalChanges % DOWNSAMPLER_POSITIONAL_UPDATE_INTERVAL == 0 ) {
for ( ReadsDownsampler<SAMRecord> perSampleDownsampler : perSampleDownsamplers.values() ) {
perSampleDownsampler.signalNoMoreReadsBefore(read);
updateEarliestPendingRead(perSampleDownsampler);
}
}
prevRead = read;
private void processFinalizedAndPendingItems( ReadsDownsampler<SAMRecord> currentDownsampler ) {
if ( currentDownsampler.hasFinalizedItems() ) {
orderedDownsampledReadsCache.addAll(currentDownsampler.consumeFinalizedItems());
}
if ( ! nestedSAMIterator.hasNext() ) {
for ( ReadsDownsampler<SAMRecord> perSampleDownsampler : perSampleDownsamplers.values() ) {
perSampleDownsampler.signalEndOfInput();
}
earliestPendingRead = null;
earliestPendingDownsampler = null;
}
for ( ReadsDownsampler<SAMRecord> perSampleDownsampler : perSampleDownsamplers.values() ) {
if ( perSampleDownsampler.hasFinalizedItems() ) {
orderedDownsampledReadsCache.addAll(perSampleDownsampler.consumeFinalizedItems());
}
}
return readyToReleaseReads();
updateEarliestPendingRead(currentDownsampler);
}
public void remove() {

3
public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java
View File

@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
/**
@ -37,6 +38,6 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
public class Platform454Filter extends ReadFilter {
public boolean filterOut(SAMRecord rec) {
return (ReadUtils.is454Read(rec));
return (ReadUtils.is454Read((GATKSAMRecord)rec));
}
}

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

@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.filters;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
/**
@ -41,7 +42,7 @@ public class PlatformFilter extends ReadFilter {
public boolean filterOut(SAMRecord rec) {
for ( String name : PLFilterNames )
if ( ReadUtils.isPlatformRead(rec, name.toUpperCase() ))
if ( ReadUtils.isPlatformRead((GATKSAMRecord)rec, name.toUpperCase() ))
return true;
return false;
}

12
public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
View File

@ -30,14 +30,14 @@ import org.broad.tribble.AbstractFeatureReader;
import org.broad.tribble.FeatureCodec;
import org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub;
import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.variant.bcf2.BCF2Utils;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.writer.Options;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.writer.Options;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
import java.io.*;
import java.util.Arrays;

2
public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
View File

@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.io.stubs;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.File;

16
public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
View File

@ -29,13 +29,13 @@ import org.broadinstitute.sting.gatk.CommandLineExecutable;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.io.OutputTracker;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.writer.Options;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.writer.Options;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
import java.io.File;
import java.io.OutputStream;
@ -232,7 +232,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
}
if ( UPDATE_CONTIG_HEADERS )
vcfHeader = VCFUtils.withUpdatedContigs(vcfHeader, engine);
vcfHeader = GATKVCFUtils.withUpdatedContigs(vcfHeader, engine);
}
outputTracker.getStorage(this).writeHeader(vcfHeader);

4
public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
View File

@ -131,7 +131,7 @@ public class GATKRunReport {
private String hostName;
@Element(required = true, name = "java")
private String java;
private String javaVersion;
@Element(required = true, name = "machine")
private String machine;
@ -212,7 +212,7 @@ public class GATKRunReport {
hostName = Utils.resolveHostname();
// basic java information
java = Utils.join("-", Arrays.asList(System.getProperty("java.vendor"), System.getProperty("java.version")));
javaVersion = Utils.join("-", Arrays.asList(System.getProperty("java.vendor"), System.getProperty("java.version")));
machine = Utils.join("-", Arrays.asList(System.getProperty("os.name"), System.getProperty("os.arch")));
// if there was an exception, capture it

2
public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
View File

@ -9,7 +9,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.variant.variantcontext.*;
import java.util.*;

4
public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java
View File

@ -33,9 +33,7 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec;
import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.AbstractVCFCodec;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.GATKDocUtils;

1
public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java
View File

@ -39,7 +39,6 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;

7
public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java
View File

@ -117,7 +117,7 @@ public class GATKReport {
* @param numColumns the number of columns in this table
*/
public void addTable(final String tableName, final String tableDescription, final int numColumns) {
addTable(tableName, tableDescription, numColumns, false);
addTable(tableName, tableDescription, numColumns, false, false);
}
/**
@ -127,9 +127,10 @@ public class GATKReport {
* @param tableDescription the description of the table
* @param numColumns the number of columns in this table
* @param sortByRowID whether to sort the rows by the row ID
* @param sortByAllColumns whether to sort the rows by all columns starting from leftmost column
*/
public void addTable(final String tableName, final String tableDescription, final int numColumns, final boolean sortByRowID) {
GATKReportTable table = new GATKReportTable(tableName, tableDescription, numColumns, sortByRowID);
public void addTable(final String tableName, final String tableDescription, final int numColumns, final boolean sortByRowID, final boolean sortByAllColumns) {
GATKReportTable table = new GATKReportTable(tableName, tableDescription, numColumns, sortByRowID, sortByAllColumns);
tables.put(tableName, table);
}

121
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
View File

@ -47,6 +47,7 @@ public class GATKReportTable {
private final String tableDescription;
private final boolean sortByRowID;
private final boolean sortByAllColumns;
private List<Object[]> underlyingData;
private final List<GATKReportColumn> columnInfo;
@ -108,6 +109,9 @@ public class GATKReportTable {
// when reading from a file, we do not re-sort the rows
sortByRowID = false;
// when reading from a file, we do not re-sort the rows
sortByAllColumns = false;
// initialize the data
final int nColumns = Integer.parseInt(tableData[TableDataHeaderFields.COLS.index()]);
final int nRows = Integer.parseInt(tableData[TableDataHeaderFields.ROWS.index()]);
@ -177,7 +181,7 @@ public class GATKReportTable {
* @param numColumns the number of columns in this table
*/
public GATKReportTable(final String tableName, final String tableDescription, final int numColumns) {
this(tableName, tableDescription, numColumns, true);
this(tableName, tableDescription, numColumns, true, false);
}
/**
@ -187,8 +191,9 @@ public class GATKReportTable {
* @param tableDescription the description of the table
* @param numColumns the number of columns in this table
* @param sortByRowID whether to sort rows by the row ID (instead of the order in which they were added)
* @param sortByAllColumns whether to sort rows by all columns (instead of the order in which they were added)
*/
public GATKReportTable(final String tableName, final String tableDescription, final int numColumns, final boolean sortByRowID) {
public GATKReportTable(final String tableName, final String tableDescription, final int numColumns, final boolean sortByRowID, final boolean sortByAllColumns) {
if ( !isValidName(tableName) ) {
throw new ReviewedStingException("Attempted to set a GATKReportTable name of '" + tableName + "'. GATKReportTable names must be purely alphanumeric - no spaces or special characters are allowed.");
}
@ -200,6 +205,7 @@ public class GATKReportTable {
this.tableName = tableName;
this.tableDescription = tableDescription;
this.sortByRowID = sortByRowID;
this.sortByAllColumns = sortByAllColumns;
underlyingData = new ArrayList<Object[]>(INITITAL_ARRAY_SIZE);
columnInfo = new ArrayList<GATKReportColumn>(numColumns);
@ -212,7 +218,7 @@ public class GATKReportTable {
* @param tableToCopy
*/
public GATKReportTable(final GATKReportTable tableToCopy, final boolean copyData) {
this(tableToCopy.getTableName(), tableToCopy.getTableDescription(), tableToCopy.getNumColumns(), tableToCopy.sortByRowID);
this(tableToCopy.getTableName(), tableToCopy.getTableDescription(), tableToCopy.getNumColumns(), tableToCopy.sortByRowID, tableToCopy.sortByAllColumns);
for ( final GATKReportColumn column : tableToCopy.getColumnInfo() )
addColumn(column.getColumnName(), column.getFormat());
if ( copyData )
@ -559,30 +565,62 @@ public class GATKReportTable {
needsPadding = true;
out.printf(column.getColumnFormat().getNameFormat(), column.getColumnName());
}
out.println();
}
out.println();
// write the table body
if ( sortByRowID ) {
// make sure that there are exactly the correct number of ID mappings
if ( rowIdToIndex.size() != underlyingData.size() )
throw new ReviewedStingException("There isn't a 1-to-1 mapping from row ID to index; this can happen when rows are not created consistently");
// write the table body
if ( sortByAllColumns ) {
Collections.sort(underlyingData, new Comparator<Object[]>() {
//INVARIANT the two arrays are of the same length and corresponding elements are of the same type
@Override
public int compare(Object[] objectArr1, Object[] objectArr2) {
final int EQUAL = 0;
final TreeMap<Object, Integer> sortedMap;
try {
sortedMap = new TreeMap<Object, Integer>(rowIdToIndex);
} catch (ClassCastException e) {
throw new ReviewedStingException("Unable to sort the rows based on the row IDs because the ID Objects are of different types");
}
for ( final Map.Entry<Object, Integer> rowKey : sortedMap.entrySet() )
writeRow(out, underlyingData.get(rowKey.getValue()));
} else {
for ( final Object[] row : underlyingData )
writeRow(out, row);
}
int result = EQUAL;
out.println();
}
int l = objectArr1.length;
for (int x = 0; x < l; x++) {
if (objectArr1[x] instanceof Integer) {
result = ((Integer)objectArr1[x]).compareTo((Integer)objectArr2[x]);
if( result != EQUAL) {
return result;
}
} else if (objectArr1[x] instanceof Double) {
result = ((Double)objectArr1[x]).compareTo((Double)objectArr2[x]);
if( result != EQUAL) {
return result;
}
} else { // default uses String comparison
result = objectArr1[x].toString().compareTo(objectArr2[x].toString());
if( result != EQUAL) {
return result;
}
}
}
return result;
}
});
for ( final Object[] row : underlyingData )
writeRow(out, row);
} else if ( sortByRowID ) {
// make sure that there are exactly the correct number of ID mappings
if ( rowIdToIndex.size() != underlyingData.size() )
throw new ReviewedStingException("There isn't a 1-to-1 mapping from row ID to index; this can happen when rows are not created consistently");
final TreeMap<Object, Integer> sortedMap;
try {
sortedMap = new TreeMap<Object, Integer>(rowIdToIndex);
} catch (ClassCastException e) {
throw new ReviewedStingException("Unable to sort the rows based on the row IDs because the ID Objects are of different types");
}
for ( final Map.Entry<Object, Integer> rowKey : sortedMap.entrySet() )
writeRow(out, underlyingData.get(rowKey.getValue()));
} else {
for ( final Object[] row : underlyingData )
writeRow(out, row);
}
out.println();
}
private void writeRow(final PrintStream out, final Object[] row) {
boolean needsPadding = false;
@ -697,8 +735,41 @@ public class GATKReportTable {
}
private List<Object[]> getOrderedRows() {
if ( !sortByRowID )
if ( sortByAllColumns ) {
Collections.sort(underlyingData, new Comparator<Object[]>() {
//INVARIANT the two arrays are of the same length and corresponding elements are of the same type
@Override
public int compare(Object[] objectArr1, Object[] objectArr2) {
final int EQUAL = 0;
int result = EQUAL;
int l = objectArr1.length;
for (int x = 0; x < l; x++) {
if (objectArr1[x] instanceof Integer) {
result = ((Integer)objectArr1[x]).compareTo((Integer)objectArr2[x]);
if( result != EQUAL) {
return result;
}
} else if (objectArr1[x] instanceof Double) {
result = ((Double)objectArr1[x]).compareTo((Double)objectArr2[x]);
if( result != EQUAL) {
return result;
}
} else { // default uses String comparison
result = objectArr1[x].toString().compareTo(objectArr2[x].toString());
if( result != EQUAL) {
return result;
}
}
}
return result;
}
});
return underlyingData;
} else if ( !sortByRowID ) {
return underlyingData;
}
final TreeMap<Object, Integer> sortedMap;
try {

2
public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java
View File

@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.samples;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.Genotype;
import java.util.*;

85
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadsNano.java
View File

@ -33,14 +33,14 @@ import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider
import org.broadinstitute.sting.gatk.datasources.providers.ReadView;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.nanoScheduler.NSMapFunction;
import org.broadinstitute.sting.utils.nanoScheduler.NSProgressFunction;
import org.broadinstitute.sting.utils.nanoScheduler.NSReduceFunction;
import org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
/**
* A nano-scheduling version of TraverseReads.
@ -54,12 +54,20 @@ import java.util.List;
*/
public class TraverseReadsNano<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,ReadShardDataProvider> {
/** our log, which we want to capture anything from this class */
private final static boolean PRE_READ_ALL_MAP_DATA = true;
protected static final Logger logger = Logger.getLogger(TraverseReadsNano.class);
private static final boolean DEBUG = false;
final NanoScheduler<MapData, MapResult, T> nanoScheduler;
public TraverseReadsNano(int nThreads) {
nanoScheduler = new NanoScheduler<MapData, MapResult, T>(nThreads);
nanoScheduler.setProgressFunction(new NSProgressFunction<MapData>() {
@Override
public void progress(MapData lastProcessedMap) {
if ( lastProcessedMap.refContext != null )
printProgress(lastProcessedMap.refContext.getLocus());
}
});
}
@Override
@ -78,7 +86,8 @@ public class TraverseReadsNano<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,
public T traverse(ReadWalker<M,T> walker,
ReadShardDataProvider dataProvider,
T sum) {
logger.debug(String.format("TraverseReadsNano.traverse Covered dataset is %s", dataProvider));
if ( logger.isDebugEnabled() )
logger.debug(String.format("TraverseReadsNano.traverse Covered dataset is %s", dataProvider));
if( !dataProvider.hasReads() )
throw new IllegalArgumentException("Unable to traverse reads; no read data is available.");
@ -87,14 +96,10 @@ public class TraverseReadsNano<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,
final TraverseReadsMap myMap = new TraverseReadsMap(walker);
final TraverseReadsReduce myReduce = new TraverseReadsReduce(walker);
final List<MapData> aggregatedInputs = aggregateMapData(dataProvider);
final T result = nanoScheduler.execute(aggregatedInputs.iterator(), myMap, sum, myReduce);
final GATKSAMRecord lastRead = aggregatedInputs.get(aggregatedInputs.size() - 1).read;
final GenomeLoc locus = engine.getGenomeLocParser().createGenomeLoc(lastRead);
final Iterator<MapData> aggregatedInputs = aggregateMapData(dataProvider);
final T result = nanoScheduler.execute(aggregatedInputs, myMap, sum, myReduce);
updateCumulativeMetrics(dataProvider.getShard());
printProgress(locus);
return result;
}
@ -107,29 +112,49 @@ public class TraverseReadsNano<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,
* @return a linked list of MapData objects holding the read, ref, and ROD info for every map/reduce
* should execute
*/
private List<MapData> aggregateMapData(final ReadShardDataProvider dataProvider) {
final ReadView reads = new ReadView(dataProvider);
final ReadReferenceView reference = new ReadReferenceView(dataProvider);
final ReadBasedReferenceOrderedView rodView = new ReadBasedReferenceOrderedView(dataProvider);
final List<MapData> mapData = new LinkedList<MapData>();
for ( final SAMRecord read : reads ) {
final ReferenceContext refContext = ! read.getReadUnmappedFlag()
? reference.getReferenceContext(read)
: null;
// if the read is mapped, create a metadata tracker
final RefMetaDataTracker tracker = read.getReferenceIndex() >= 0
? rodView.getReferenceOrderedDataForRead(read)
: null;
// update the number of reads we've seen
dataProvider.getShard().getReadMetrics().incrementNumIterations();
mapData.add(new MapData((GATKSAMRecord)read, refContext, tracker));
private Iterator<MapData> aggregateMapData(final ReadShardDataProvider dataProvider) {
final Iterator<MapData> it = makeDataIterator(dataProvider);
if ( PRE_READ_ALL_MAP_DATA ) {
final LinkedList<MapData> l = new LinkedList<MapData>();
while ( it.hasNext() ) l.add(it.next());
return l.iterator();
} else {
return it;
}
}
return mapData;
private Iterator<MapData> makeDataIterator(final ReadShardDataProvider dataProvider) {
return new Iterator<MapData> () {
final ReadView reads = new ReadView(dataProvider);
final ReadReferenceView reference = new ReadReferenceView(dataProvider);
final ReadBasedReferenceOrderedView rodView = new ReadBasedReferenceOrderedView(dataProvider);
final Iterator<SAMRecord> readIterator = reads.iterator();
@Override public boolean hasNext() { return readIterator.hasNext(); }
@Override
public MapData next() {
final SAMRecord read = readIterator.next();
final ReferenceContext refContext = ! read.getReadUnmappedFlag()
? reference.getReferenceContext(read)
: null;
// if the read is mapped, create a metadata tracker
final RefMetaDataTracker tracker = read.getReferenceIndex() >= 0
? rodView.getReferenceOrderedDataForRead(read)
: null;
// update the number of reads we've seen
dataProvider.getShard().getReadMetrics().incrementNumIterations();
return new MapData((GATKSAMRecord)read, refContext, tracker);
}
@Override public void remove() {
throw new UnsupportedOperationException("Remove not supported");
}
};
}
@Override

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

@ -37,7 +37,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.clipping.ClippingOp;
import org.broadinstitute.sting.utils.clipping.ClippingRepresentation;

10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
View File

@ -32,12 +32,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

12
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
View File

@ -8,12 +8,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAn
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.Collection;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
View File

@ -37,10 +37,10 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
View File

@ -2,11 +2,11 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Allele;
import java.util.*;

12
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
View File

@ -35,12 +35,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextUtils;
import java.util.*;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
View File

@ -1,12 +1,12 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Allele;
import java.util.*;

10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
View File

@ -8,13 +8,13 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

14
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
View File

@ -7,17 +7,17 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
View File

@ -34,13 +34,13 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
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@ -8,11 +8,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

12
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
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@ -33,20 +33,20 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.io.Serializable;
import java.util.*;

10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
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@ -9,11 +9,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.WorkInProgressAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
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@ -7,9 +7,9 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
View File

@ -10,11 +10,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*;

66
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
View File

@ -1,66 +0,0 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.IndelUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.*;
/**
* Rough category of indel type (insertion, deletion, multi-allelic, other)
*/
public class IndelType extends InfoFieldAnnotation implements ExperimentalAnnotation {
public Map<String, Object> annotate(final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,
final ReferenceContext ref,
final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc,
final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
int run;
if (vc.isMixed()) {
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%s", "MIXED"));
return map;
}
else if ( vc.isIndel() ) {
String type="";
if (!vc.isBiallelic())
type = "MULTIALLELIC_INDEL";
else {
if (vc.isSimpleInsertion())
type = "INS.";
else if (vc.isSimpleDeletion())
type = "DEL.";
else
type = "OTHER.";
ArrayList<Integer> inds = IndelUtils.findEventClassificationIndex(vc, ref);
for (int k : inds) {
type = type+ IndelUtils.getIndelClassificationName(k)+".";
}
}
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%s", type));
return map;
} else {
return null;
}
}
public List<String> getKeyNames() { return Arrays.asList("IndelType"); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("IndelType", 1, VCFHeaderLineType.String, "Indel type description")); }
}

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
View File

@ -6,10 +6,10 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
View File

@ -11,10 +11,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MendelianViolation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
View File

@ -2,12 +2,12 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Allele;
import java.util.*;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
View File

@ -8,13 +8,13 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

12
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
View File

@ -31,14 +31,14 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.List;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
View File

@ -7,11 +7,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
View File

@ -6,11 +6,11 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
View File

@ -8,11 +8,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
View File

@ -10,12 +10,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnota
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*;

10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
View File

@ -10,14 +10,14 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MannWhitneyU;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
View File

@ -7,14 +7,14 @@ import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Allele;
import java.util.*;

10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
View File

@ -31,11 +31,11 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFHeaderLineCount;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

7
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
View File

@ -35,9 +35,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*;
@ -212,7 +213,7 @@ public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotatio
// Make sure that the SnpEff version number and command-line header lines are present in the VCF header of
// the SnpEff rod, and that the file was generated by a supported version of SnpEff:
VCFHeader snpEffVCFHeader = VCFUtils.getVCFHeadersFromRods(toolkit, Arrays.asList(snpEffRodBinding.getName())).get(snpEffRodBinding.getName());
VCFHeader snpEffVCFHeader = GATKVCFUtils.getVCFHeadersFromRods(toolkit, Arrays.asList(snpEffRodBinding.getName())).get(snpEffRodBinding.getName());
VCFHeaderLine snpEffVersionLine = snpEffVCFHeader.getOtherHeaderLine(SNPEFF_VCF_HEADER_VERSION_LINE_KEY);
VCFHeaderLine snpEffCommandLine = snpEffVCFHeader.getOtherHeaderLine(SNPEFF_VCF_HEADER_COMMAND_LINE_KEY);

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
View File

@ -7,10 +7,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

12
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
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@ -31,12 +31,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineCount;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;
@ -57,7 +57,7 @@ public class TandemRepeatAnnotator extends InfoFieldAnnotation implements Standa
if ( !vc.isIndel())
return null;
Pair<List<Integer>,byte[]> result = VariantContextUtils.getNumTandemRepeatUnits(vc, ref.getForwardBases());
Pair<List<Integer>,byte[]> result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, ref.getForwardBases());
if (result == null)
return null;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
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@ -8,12 +8,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
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@ -10,11 +10,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineCount;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*;

13
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -35,13 +35,14 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import java.util.*;
@ -225,7 +226,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
// note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(engine.getVCFAnnotationDescriptions());
for ( VCFHeaderLine line : VCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variantCollection.variants.getName())) ) {
for ( VCFHeaderLine line : GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variantCollection.variants.getName())) ) {
if ( isUniqueHeaderLine(line, hInfo) )
hInfo.add(line);
}
@ -237,7 +238,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
continue;
}
VCFInfoHeaderLine targetHeaderLine = null;
for ( VCFHeaderLine line : VCFUtils.getHeaderFields(getToolkit(), Arrays.asList(expression.binding.getName())) ) {
for ( VCFHeaderLine line : GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(expression.binding.getName())) ) {
if ( line instanceof VCFInfoHeaderLine ) {
VCFInfoHeaderLine infoline = (VCFInfoHeaderLine)line;
if ( infoline.getID().equals(expression.fieldName) ) {

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -32,9 +32,9 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.variant.variantcontext.*;
import java.util.*;

60
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java 100755
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@ -0,0 +1,60 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.IndelUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*;
/**
* Assigns a roughly correct category of the variant type (SNP, MNP, insertion, deletion, etc.)
*/
public class VariantType extends InfoFieldAnnotation implements ExperimentalAnnotation {
public Map<String, Object> annotate(final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,
final ReferenceContext ref,
final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc,
final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
StringBuffer type = new StringBuffer("");
if ( vc.isVariant() && !vc.isBiallelic() )
type.append("MULTIALLELIC_");
if ( !vc.isIndel() ) {
type.append(vc.getType().toString());
} else {
if (vc.isSimpleInsertion())
type.append("INSERTION.");
else if (vc.isSimpleDeletion())
type.append("DELETION.");
else
type.append("COMPLEX.");
ArrayList<Integer> inds = IndelUtils.findEventClassificationIndex(vc, ref);
type.append(IndelUtils.getIndelClassificationName(inds.get(0)));
for (int i = 1; i < inds.size(); i++ ) {
type.append(".");
type.append(IndelUtils.getIndelClassificationName(inds.get(i)));
}
}
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%s", type));
return map;
}
public List<String> getKeyNames() { return Arrays.asList("VariantType"); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("VariantType", 1, VCFHeaderLineType.String, "Variant type description")); }
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
View File

@ -1,8 +1,8 @@
package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.List;
import java.util.Map;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java
View File

@ -1,7 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.List;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
View File

@ -4,10 +4,10 @@ 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.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.List;

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