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Merge branch 'master' into intervals

This commit is contained in:
Eric Banks 2011-11-09 15:27:15 -05:00
parent d64f8a89a9 f080f64f99
commit 8205efbb29
8 changed files with 106 additions and 44 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
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@ -33,18 +33,18 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements Experiment
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( mendelianViolation == null ) {
if ( walker instanceof VariantAnnotator ) {
if ( walker instanceof VariantAnnotator && ((VariantAnnotator) walker).familyStr != null) {
mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).familyStr, ((VariantAnnotator)walker).minGenotypeQualityP );
}
else {
throw new UserException("Mendelian violation annotation can only be used from the Variant Annotator");
throw new UserException("Mendelian violation annotation can only be used from the Variant Annotator, and must be provided a valid Family String file (-family) on the command line.");
}
}
Map<String,Object> toRet = new HashMap<String,Object>(1);
boolean hasAppropriateGenotypes = vc.hasGenotype(mendelianViolation.getSampleChild()) &&
vc.hasGenotype(mendelianViolation.getSampleDad()) &&
vc.hasGenotype(mendelianViolation.getSampleMom());
boolean hasAppropriateGenotypes = vc.hasGenotype(mendelianViolation.getSampleChild()) && vc.getGenotype(mendelianViolation.getSampleChild()).hasLikelihoods() &&
vc.hasGenotype(mendelianViolation.getSampleDad()) && vc.getGenotype(mendelianViolation.getSampleDad()).hasLikelihoods() &&
vc.hasGenotype(mendelianViolation.getSampleMom()) && vc.getGenotype(mendelianViolation.getSampleMom()).hasLikelihoods();
if ( hasAppropriateGenotypes )
toRet.put("MVLR",mendelianViolation.violationLikelihoodRatio(vc));

16
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -528,10 +528,10 @@ public class PairHMMIndelErrorModel {
}
else {
byte[] readBases = Arrays.copyOfRange(unclippedReadBases,numStartClippedBases,
final byte[] readBases = Arrays.copyOfRange(unclippedReadBases,numStartClippedBases,
unclippedReadBases.length-numEndClippedBases);
byte[] readQuals = Arrays.copyOfRange(unclippedReadQuals,numStartClippedBases,
final byte[] readQuals = Arrays.copyOfRange(unclippedReadQuals,numStartClippedBases,
unclippedReadBases.length-numEndClippedBases);
int j=0;
@ -540,6 +540,7 @@ public class PairHMMIndelErrorModel {
double[][] matchMetricArray = null, XMetricArray = null, YMetricArray = null;
byte[] previousHaplotypeSeen = null;
double[] previousGOP = null;
double[] previousGCP = null;
int startIdx;
for (Allele a: haplotypeMap.keySet()) {
@ -555,7 +556,7 @@ public class PairHMMIndelErrorModel {
long indStart = start - haplotype.getStartPosition();
long indStop = stop - haplotype.getStartPosition();
byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBases(),
final byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBases(),
(int)indStart, (int)indStop);
double readLikelihood;
@ -572,13 +573,14 @@ public class PairHMMIndelErrorModel {
if (previousHaplotypeSeen == null)
startIdx = 0;
else {
int s1 = computeFirstDifferingPosition(haplotypeBases, previousHaplotypeSeen);
int s2 = computeFirstDifferingPosition(currentContextGOP, previousGOP);
startIdx = Math.min(s1,s2);
final int s1 = computeFirstDifferingPosition(haplotypeBases, previousHaplotypeSeen);
final int s2 = computeFirstDifferingPosition(currentContextGOP, previousGOP);
final int s3 = computeFirstDifferingPosition(currentContextGCP, previousGCP);
startIdx = Math.min(Math.min(s1, s2), s3);
}
previousHaplotypeSeen = haplotypeBases.clone();
previousGOP = currentContextGOP.clone();
previousGCP = currentContextGCP.clone();
readLikelihood = computeReadLikelihoodGivenHaplotypeAffineGaps(haplotypeBases, readBases, readQuals,

6
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -556,9 +556,9 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
if (vc == null)
return false;
// if we're not looking at specific samples then the absense of a compVC means discordance
if (NO_SAMPLES_SPECIFIED && (compVCs == null || compVCs.isEmpty()))
return true;
// if we're not looking at specific samples then the absence of a compVC means discordance
if (NO_SAMPLES_SPECIFIED)
return (compVCs == null || compVCs.isEmpty());
// check if we find it in the variant rod
Map<String, Genotype> genotypes = vc.getGenotypes(samples);

20
public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
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@ -58,15 +58,6 @@ public class ReadClipper {
return hardClipByReferenceCoordinates(refStart, -1);
}
private int numDeletions(GATKSAMRecord read) {
int result = 0;
for (CigarElement e: read.getCigar().getCigarElements()) {
if ( e.getOperator() == CigarOperator.DELETION || e.getOperator() == CigarOperator.D )
result =+ e.getLength();
}
return result;
}
protected GATKSAMRecord hardClipByReferenceCoordinates(int refStart, int refStop) {
int start = (refStart < 0) ? 0 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart, ReadUtils.ClippingTail.RIGHT_TAIL);
int stop = (refStop < 0) ? read.getReadLength() - 1 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop, ReadUtils.ClippingTail.LEFT_TAIL);
@ -90,7 +81,7 @@ public class ReadClipper {
@Requires("left <= right")
public GATKSAMRecord hardClipBothEndsByReferenceCoordinates(int left, int right) {
if (left == right)
if (read.isEmpty() || left == right)
return new GATKSAMRecord(read.getHeader());
GATKSAMRecord leftTailRead = hardClipByReferenceCoordinates(right, -1);
@ -104,6 +95,9 @@ public class ReadClipper {
}
public GATKSAMRecord hardClipLowQualEnds(byte lowQual) {
if (read.isEmpty())
return read;
byte [] quals = read.getBaseQualities();
int leftClipIndex = 0;
int rightClipIndex = read.getReadLength() - 1;
@ -126,6 +120,9 @@ public class ReadClipper {
}
public GATKSAMRecord hardClipSoftClippedBases () {
if (read.isEmpty())
return read;
int readIndex = 0;
int cutLeft = -1; // first position to hard clip (inclusive)
int cutRight = -1; // first position to hard clip (inclusive)
@ -182,6 +179,9 @@ public class ReadClipper {
}
public GATKSAMRecord hardClipLeadingInsertions() {
if (read.isEmpty())
return read;
for(CigarElement cigarElement : read.getCigar().getCigarElements()) {
if (cigarElement.getOperator() != CigarOperator.HARD_CLIP && cigarElement.getOperator() != CigarOperator.SOFT_CLIP &&
cigarElement.getOperator() != CigarOperator.INSERTION && cigarElement.getOperator() != CigarOperator.DELETION)

6
public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
View File

@ -87,7 +87,13 @@ public class TableCodec implements ReferenceDependentFeatureCodec {
public Object readHeader(LineReader reader) {
String line = "";
try {
boolean isFirst = true;
while ((line = reader.readLine()) != null) {
System.out.println(line);
if ( isFirst && ! line.startsWith(headerDelimiter) ) {
throw new UserException.MalformedFile("TableCodec file does not have a header");
}
isFirst &= false;
if (line.startsWith(headerDelimiter)) {
if (header.size() > 0) throw new IllegalStateException("Input table file seems to have two header lines. The second is = " + line);
String spl[] = line.split(delimiterRegex);

6
public/java/src/org/broadinstitute/sting/utils/codecs/table/TableFeature.java
View File

@ -1,7 +1,9 @@
package org.broadinstitute.sting.utils.codecs.table;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils;
import java.util.List;
@ -44,6 +46,10 @@ public class TableFeature implements Feature {
return values.get(columnPosition);
}
public String toString() {
return String.format("%s\t%s",position.toString(), Utils.join("\t",values));
}
public String get(String columnName) {
int position = keys.indexOf(columnName);
if (position < 0) throw new IllegalArgumentException("We don't have a column named " + columnName);

73
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
View File

@ -24,7 +24,10 @@
package org.broadinstitute.sting.utils.sam;
import net.sf.samtools.*;
import net.sf.samtools.BAMRecord;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.NGSPlatform;
import java.util.HashMap;
@ -83,8 +86,13 @@ public class GATKSAMRecord extends BAMRecord {
read.getMateReferenceIndex(),
read.getMateAlignmentStart(),
read.getInferredInsertSize(),
new byte[]{});
super.clearAttributes();
null);
SAMReadGroupRecord samRG = read.getReadGroup();
clearAttributes();
if (samRG != null) {
GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(samRG);
setReadGroup(rg);
}
}
public GATKSAMRecord(final SAMFileHeader header,
@ -131,6 +139,21 @@ public class GATKSAMRecord extends BAMRecord {
return mReadGroup;
}
@Override
public int hashCode() {
return super.hashCode();
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (!(o instanceof GATKSAMRecord)) return false;
// note that we do not consider the GATKSAMRecord internal state at all
return super.equals(o);
}
/**
* Efficient caching accessor that returns the GATK NGSPlatform of this read
* @return
@ -144,11 +167,9 @@ public class GATKSAMRecord extends BAMRecord {
retrievedReadGroup = true;
}
//
//
// Reduced read functions
//
//
///////////////////////////////////////////////////////////////////////////////
// *** ReduceReads functions ***//
///////////////////////////////////////////////////////////////////////////////
public byte[] getReducedReadCounts() {
if ( ! retrievedReduceReadCounts ) {
@ -167,6 +188,12 @@ public class GATKSAMRecord extends BAMRecord {
return getReducedReadCounts()[i];
}
///////////////////////////////////////////////////////////////////////////////
// *** GATKSAMRecord specific methods ***//
///////////////////////////////////////////////////////////////////////////////
/**
* Checks whether an attribute has been set for the given key.
*
@ -220,18 +247,26 @@ public class GATKSAMRecord extends BAMRecord {
return null;
}
@Override
public int hashCode() {
return super.hashCode();
/**
* Checks whether if the read has any bases.
*
* Empty reads can be dangerous as it may have no cigar strings, no read names and
* other missing attributes.
*
* @return true if the read has no bases
*/
public boolean isEmpty() {
return this.getReadLength() == 0;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (!(o instanceof GATKSAMRecord)) return false;
// note that we do not consider the GATKSAMRecord internal state at all
return super.equals(o);
/**
* Clears all attributes except ReadGroup of the read.
*/
public void simplify () {
GATKSAMReadGroupRecord rg = getReadGroup();
this.clearAttributes();
setReadGroup(rg);
}
}

13
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -64,6 +64,19 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
executeTest("testDiscordance--" + testFile, spec);
}
@Test
public void testDiscordanceNoSampleSpecified() {
String testFile = validationDataLocation + "NA12878.hg19.example1.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + hg19Reference + " -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s -NO_HEADER",
1,
Arrays.asList("5d7d899c0c4954ec59104aebfe4addd5")
);
executeTest("testDiscordanceNoSampleSpecified--" + testFile, spec);
}
@Test
public void testConcordance() {
String testFile = validationDataLocation + "NA12878.hg19.example1.vcf";