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Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Mark DePristo 2011-11-07 13:26:37 -05:00
parent 63eeb5a56c 759f4fe6b8
commit bb448b27d2
22 changed files with 60 additions and 239 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java
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@ -131,7 +131,7 @@ public class AlignmentContextUtils {
}
}
public static Map<String, AlignmentContext> splitContextBySampleName(ReadBackedPileup pileup, String assumedSingleSample) {
public static Map<String, AlignmentContext> splitContextBySampleName(ReadBackedPileup pileup) {
return splitContextBySampleName(new AlignmentContext(pileup.getLocation(), pileup));
}

3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
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@ -14,7 +14,8 @@ import java.util.List;
/**
* The phred-scaled p-value (u-based z-approximation) from the Mann-Whitney Rank Sum Test for base qualities (ref bases vs. bases of the alternate allele)
* The phred-scaled p-value (u-based z-approximation) from the Mann-Whitney Rank Sum Test for base qualities (ref bases vs. bases of the alternate allele).
* Note that the base quality rank sum test can not be calculated for homozygous sites.
*/
public class BaseQualityRankSumTest extends RankSumTest {
public List<String> getKeyNames() { return Arrays.asList("BaseQRankSum"); }

3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
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@ -46,7 +46,8 @@ import java.util.*;
/**
* Phred-scaled p-value using Fisher's Exact Test to detect strand bias (the variation
* being seen on only the forward or only the reverse strand) in the reads? More bias is
* indicative of false positive calls.
* indicative of false positive calls. Note that the fisher strand test may not be
* calculated for certain complex indel cases or for multi-allelic sites.
*/
public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotation {
private static final String FS = "FS";

12
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
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@ -52,6 +52,8 @@ import java.util.*;
/**
* Consistency of the site with two (and only two) segregating haplotypes. Higher scores
* are indicative of regions with bad alignments, often leading to artifactual SNP and indel calls.
* Note that the Haplotype Score is only calculated for sites with read coverage; also, for SNPs, the
* site must be bi-allelic.
*/
public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnotation {
private final static boolean DEBUG = false;
@ -180,12 +182,12 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
final Haplotype haplotype1 = consensusHaplotypeQueue.poll();
List<Haplotype>hlist = new ArrayList<Haplotype>();
hlist.add(new Haplotype(haplotype1.getBasesAsBytes(), 60));
hlist.add(new Haplotype(haplotype1.getBases(), 60));
for (int k=1; k < haplotypesToCompute; k++) {
Haplotype haplotype2 = consensusHaplotypeQueue.poll();
if(haplotype2 == null ) { haplotype2 = haplotype1; } // Sometimes only the reference haplotype can be found
hlist.add(new Haplotype(haplotype2.getBasesAsBytes(), 20));
hlist.add(new Haplotype(haplotype2.getBases(), 20));
}
return hlist;
} else
@ -229,8 +231,8 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
}
private Haplotype getConsensusHaplotype(final Haplotype haplotypeA, final Haplotype haplotypeB) {
final byte[] a = haplotypeA.getBasesAsBytes();
final byte[] b = haplotypeB.getBasesAsBytes();
final byte[] a = haplotypeA.getBases();
final byte[] b = haplotypeB.getBases();
if (a.length != b.length) {
throw new ReviewedStingException("Haplotypes a and b must be of same length");
@ -313,7 +315,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
// actually be a miscall in a matching direction, which would happen at a e / 3 rate. If b != c, then
// the chance that it is actually a mismatch is 1 - e, since any of the other 3 options would be a mismatch.
// so the probability-weighted mismatch rate is sum_i ( matched ? e_i / 3 : 1 - e_i ) for i = 1 ... n
final byte[] haplotypeBases = haplotype.getBasesAsBytes();
final byte[] haplotypeBases = haplotype.getBases();
final SAMRecord read = p.getRead();
byte[] readBases = read.getReadBases();

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

@ -23,7 +23,8 @@ import java.util.Map;
*
* A continuous generalization of the Hardy-Weinberg test for disequilibrium that works
* well with limited coverage per sample. See the 1000 Genomes Phase I release for
* more information.
* more information. Note that the Inbreeding Coefficient will not be calculated for files
* with fewer than a minimum (generally 10) number of samples.
*/
public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnnotation {

1
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
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@ -16,6 +16,7 @@ import java.util.List;
/**
* The phred-scaled p-value (u-based z-approximation) from the Mann-Whitney Rank Sum Test for mapping qualities (reads with ref bases vs. those with the alternate allele)
* Note that the mapping quality rank sum test can not be calculated for homozygous sites.
*/
public class MappingQualityRankSumTest extends RankSumTest {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
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@ -19,7 +19,8 @@ import java.util.Map;
/**
* Variant confidence (given as (AB+BB)/AA from the PLs) / unfiltered depth.
*
* Low scores are indicative of false positive calls and artifacts.
* Low scores are indicative of false positive calls and artifacts. Note that QualByDepth requires sequencing
* reads associated with the samples with polymorphic genotypes.
*/
public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotation {

1
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
View File

@ -20,6 +20,7 @@ import java.util.List;
/**
* The phred-scaled p-value (u-based z-approximation) from the Mann-Whitney Rank Sum Test for the distance from the end of the read for reads with the alternate allele; if the alternate allele is only seen near the ends of reads this is indicative of error).
* Note that the read position rank sum test can not be calculated for homozygous sites.
*/
public class ReadPosRankSumTest extends RankSumTest {

13
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
View File

@ -164,10 +164,6 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
@Argument(fullName="list", shortName="ls", doc="List the available annotations and exit")
protected Boolean LIST = false;
@Hidden
@Argument(fullName = "assume_single_sample_reads", shortName = "single_sample", doc = "The single sample that we should assume is represented in the input bam (and therefore associate with all reads regardless of whether they have read groups)", required = false)
protected String ASSUME_SINGLE_SAMPLE = null;
@Hidden
@Argument(fullName="vcfContainsOnlyIndels", shortName="dels",doc="Use if you are annotating an indel vcf, currently VERY experimental", required = false)
protected boolean indelsOnly = false;
@ -213,11 +209,6 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
List<String> rodName = Arrays.asList(variantCollection.variants.getName());
Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), rodName);
// if there are no valid samples, warn the user
if ( samples.size() == 0 ) {
logger.warn("There are no samples input at all; use the --sampleName argument to specify one if desired.");
}
if ( USE_ALL_ANNOTATIONS )
engine = new VariantAnnotatorEngine(annotationsToExclude, this, getToolkit());
else
@ -301,9 +292,9 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
Map<String, AlignmentContext> stratifiedContexts;
if ( BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 ) {
if ( ! context.hasExtendedEventPileup() ) {
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(context.getBasePileup(), ASSUME_SINGLE_SAMPLE);
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(context.getBasePileup());
} else {
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(context.getExtendedEventPileup(), ASSUME_SINGLE_SAMPLE);
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(context.getExtendedEventPileup());
}
if ( stratifiedContexts != null ) {
annotatedVCs = new ArrayList<VariantContext>(VCs.size());

8
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
View File

@ -39,7 +39,6 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.HashSet;
import java.util.Set;
import java.util.TreeSet;
/**
@ -71,12 +70,7 @@ public class UGCalcLikelihoods extends LocusWalker<VariantCallContext, Integer>
public void initialize() {
// get all of the unique sample names
// if we're supposed to assume a single sample, do so
Set<String> samples = new TreeSet<String>();
if ( UAC.ASSUME_SINGLE_SAMPLE != null )
samples.add(UAC.ASSUME_SINGLE_SAMPLE);
else
samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
Set<String> samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples);

6
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -96,11 +96,6 @@ public class UnifiedArgumentCollection {
@Input(fullName="alleles", shortName = "alleles", doc="The set of alleles at which to genotype when in GENOTYPE_MODE = GENOTYPE_GIVEN_ALLELES", required=false)
public RodBinding<VariantContext> alleles;
// control the error modes
@Hidden
@Argument(fullName = "assume_single_sample_reads", shortName = "single_sample", doc = "The single sample that we should assume is represented in the input bam (and therefore associate with all reads regardless of whether they have read groups)", required = false)
public String ASSUME_SINGLE_SAMPLE = null;
/**
* The minimum confidence needed in a given base for it to be used in variant calling. Note that the base quality of a base
* is capped by the mapping quality so that bases on reads with low mapping quality may get filtered out depending on this value.
@ -170,7 +165,6 @@ public class UnifiedArgumentCollection {
uac.GenotypingMode = GenotypingMode;
uac.OutputMode = OutputMode;
uac.COMPUTE_SLOD = COMPUTE_SLOD;
uac.ASSUME_SINGLE_SAMPLE = ASSUME_SINGLE_SAMPLE;
uac.STANDARD_CONFIDENCE_FOR_CALLING = STANDARD_CONFIDENCE_FOR_CALLING;
uac.STANDARD_CONFIDENCE_FOR_EMITTING = STANDARD_CONFIDENCE_FOR_EMITTING;
uac.MIN_BASE_QUALTY_SCORE = MIN_BASE_QUALTY_SCORE;

7
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -206,12 +206,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
**/
public void initialize() {
// get all of the unique sample names
// if we're supposed to assume a single sample, do so
Set<String> samples = new TreeSet<String>();
if ( UAC.ASSUME_SINGLE_SAMPLE != null )
samples.add(UAC.ASSUME_SINGLE_SAMPLE);
else
samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
Set<String> samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
// initialize the verbose writer
if ( verboseWriter != null )

17
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -106,12 +106,7 @@ public class UnifiedGenotyperEngine {
// ---------------------------------------------------------------------------------------------------------
@Requires({"toolkit != null", "UAC != null"})
public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC) {
this(toolkit, UAC, Logger.getLogger(UnifiedGenotyperEngine.class), null, null,
// get the number of samples
// if we're supposed to assume a single sample, do so
UAC.ASSUME_SINGLE_SAMPLE != null ?
new TreeSet<String>(Arrays.asList(UAC.ASSUME_SINGLE_SAMPLE)) :
SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()));
this(toolkit, UAC, Logger.getLogger(UnifiedGenotyperEngine.class), null, null, SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()));
}
@Requires({"toolkit != null", "UAC != null", "logger != null", "samples != null && samples.size() > 0"})
@ -253,7 +248,7 @@ public class UnifiedGenotyperEngine {
pileup = rawContext.getExtendedEventPileup();
else if (rawContext.hasBasePileup())
pileup = rawContext.getBasePileup();
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup, UAC.ASSUME_SINGLE_SAMPLE);
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
vc = annotationEngine.annotateContext(tracker, ref, stratifiedContexts, vc);
}
@ -435,7 +430,7 @@ public class UnifiedGenotyperEngine {
pileup = rawContext.getExtendedEventPileup();
else if (rawContext.hasBasePileup())
pileup = rawContext.getBasePileup();
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup, UAC.ASSUME_SINGLE_SAMPLE);
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
vcCall = annotationEngine.annotateContext(tracker, refContext, stratifiedContexts, vcCall);
}
@ -569,7 +564,7 @@ public class UnifiedGenotyperEngine {
return null;
// stratify the AlignmentContext and cut by sample
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup, UAC.ASSUME_SINGLE_SAMPLE);
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
} else {
@ -586,12 +581,12 @@ public class UnifiedGenotyperEngine {
return null;
// stratify the AlignmentContext and cut by sample
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup, UAC.ASSUME_SINGLE_SAMPLE);
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
}
} else if ( model == GenotypeLikelihoodsCalculationModel.Model.SNP ) {
// stratify the AlignmentContext and cut by sample
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(rawContext.getBasePileup(), UAC.ASSUME_SINGLE_SAMPLE);
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(rawContext.getBasePileup());
if( !(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) ) {
int numDeletions = 0;

18
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
View File

@ -205,7 +205,7 @@ public class HaplotypeIndelErrorModel {
byte haplotypeBase;
if (haplotypeIndex < RIGHT_ALIGN_INDEX)
haplotypeBase = haplotype.getBasesAsBytes()[haplotypeIndex];
haplotypeBase = haplotype.getBases()[haplotypeIndex];
else
haplotypeBase = (byte)0; // dummy
@ -217,7 +217,7 @@ public class HaplotypeIndelErrorModel {
if (readQual > 3)
pRead += pBaseRead;
haplotypeIndex++;
if (haplotypeIndex >= haplotype.getBasesAsBytes().length)
if (haplotypeIndex >= haplotype.getBases().length)
haplotypeIndex = RIGHT_ALIGN_INDEX;
//System.out.format("H:%c R:%c RQ:%d HI:%d %4.5f %4.5f\n", haplotypeBase, readBase, (int)readQual, haplotypeIndex, pBaseRead, pRead);
}
@ -227,8 +227,8 @@ public class HaplotypeIndelErrorModel {
System.out.println(read.getReadName());
System.out.print("Haplotype:");
for (int k=0; k <haplotype.getBasesAsBytes().length; k++) {
System.out.format("%c ", haplotype.getBasesAsBytes()[k]);
for (int k=0; k <haplotype.getBases().length; k++) {
System.out.format("%c ", haplotype.getBases()[k]);
}
System.out.println();
@ -246,8 +246,8 @@ public class HaplotypeIndelErrorModel {
System.out.println("Haplotype:");
for (int k=initialIndexInHaplotype; k <haplotype.getBasesAsBytes().length; k++) {
System.out.format("%c ", haplotype.getBasesAsBytes()[k]);
for (int k=initialIndexInHaplotype; k <haplotype.getBases().length; k++) {
System.out.format("%c ", haplotype.getBases()[k]);
}
System.out.println();
@ -275,7 +275,7 @@ public class HaplotypeIndelErrorModel {
byte haplotypeBase;
if (indX > LEFT_ALIGN_INDEX && indX < RIGHT_ALIGN_INDEX)
haplotypeBase = haplotype.getBasesAsBytes()[indX-1];
haplotypeBase = haplotype.getBases()[indX-1];
else
haplotypeBase = readBase;
@ -296,8 +296,8 @@ public class HaplotypeIndelErrorModel {
System.out.println(read.getReadName());
System.out.print("Haplotype:");
for (int k=0; k <haplotype.getBasesAsBytes().length; k++) {
System.out.format("%c ", haplotype.getBasesAsBytes()[k]);
for (int k=0; k <haplotype.getBases().length; k++) {
System.out.format("%c ", haplotype.getBases()[k]);
}
System.out.println();

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

@ -817,7 +817,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// For now, we will just arbitrarily add 10 to the mapping quality. [EB, 6/7/2010].
// TODO -- we need a better solution here
GATKSAMRecord read = aRead.getRead();
read.setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + 10, 254));
if ( read.getMappingQuality() != 255 ) // 255 == Unknown, so don't modify it
read.setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + 10, 254));
// before we fix the attribute tags we first need to make sure we have enough of the reference sequence
int neededBasesToLeft = leftmostIndex - read.getAlignmentStart();

4
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
View File

@ -381,7 +381,7 @@ public class PairHMMIndelErrorModel {
// todo -- refactor into separate function
for (Allele a: haplotypeMap.keySet()) {
Haplotype haplotype = haplotypeMap.get(a);
byte[] haplotypeBases = haplotype.getBasesAsBytes();
byte[] haplotypeBases = haplotype.getBases();
double[] contextLogGapOpenProbabilities = new double[haplotypeBases.length];
double[] contextLogGapContinuationProbabilities = new double[haplotypeBases.length];
@ -555,7 +555,7 @@ public class PairHMMIndelErrorModel {
long indStart = start - haplotype.getStartPosition();
long indStop = stop - haplotype.getStartPosition();
byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBasesAsBytes(),
byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBases(),
(int)indStart, (int)indStop);
double readLikelihood;

118
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java
View File

@ -1,118 +0,0 @@
package org.broadinstitute.sting.gatk.walkers.phasing;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.RodBinding;
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.RodWalker;
import org.broadinstitute.sting.utils.SampleUtils;
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.codecs.vcf.VCFWriter;
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.VariantContextUtils;
import java.util.*;
/**
* Merges read-back-phased and phase-by-transmission files.
*/
public class MergeAndMatchHaplotypes extends RodWalker<Integer, Integer> {
@Output
protected VCFWriter vcfWriter = null;
@Input(fullName="pbt", shortName = "pbt", doc="Input VCF truth file", required=true)
public RodBinding<VariantContext> pbtTrack;
@Input(fullName="rbp", shortName = "rbp", doc="Input VCF truth file", required=true)
public RodBinding<VariantContext> rbpTrack;
private Map<String, Genotype> pbtCache = new HashMap<String, Genotype>();
private Map<String, Genotype> rbpCache = new HashMap<String, Genotype>();
private final String SOURCE_NAME = "MergeReadBackedAndTransmissionPhasedVariants";
public void initialize() {
ArrayList<String> rodNames = new ArrayList<String>();
rodNames.add(pbtTrack.getName());
Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
Set<VCFHeaderLine> headerLines = new HashSet<VCFHeaderLine>();
headerLines.addAll(VCFUtils.getHeaderFields(this.getToolkit()));
vcfWriter.writeHeader(new VCFHeader(headerLines, vcfSamples));
}
@Override
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (tracker != null) {
Collection<VariantContext> pbts = tracker.getValues(pbtTrack, ref.getLocus());
Collection<VariantContext> rbps = tracker.getValues(rbpTrack, ref.getLocus());
VariantContext pbt = pbts.iterator().hasNext() ? pbts.iterator().next() : null;
VariantContext rbp = rbps.iterator().hasNext() ? rbps.iterator().next() : null;
if (pbt != null && rbp != null) {
Map<String, Genotype> genotypes = pbt.getGenotypes();
if (!rbp.isFiltered()) {
for (String sample : rbp.getSampleNames()) {
Genotype rbpg = rbp.getGenotype(sample);
Genotype pbtg = pbt.getGenotype(sample);
// Propagate read-backed phasing information to genotypes unphased by transmission
//if (!pbtg.isPhased() && rbpCache.containsKey(sample)) {
if (!pbtg.isPhased() && rbpg.isPhased() && rbpCache.containsKey(sample)) {
boolean orientationMatches = rbpCache.get(sample).sameGenotype(pbtCache.get(sample), false);
if (orientationMatches) {
pbtg = rbpg;
} else {
List<Allele> fwdAlleles = rbpg.getAlleles();
List<Allele> revAlleles = new ArrayList<Allele>();
for (int i = fwdAlleles.size() - 1; i >= 0; i--) {
revAlleles.add(fwdAlleles.get(i));
}
pbtg = new Genotype(sample, revAlleles, rbpg.getNegLog10PError(), rbpg.getFilters(), rbpg.getAttributes(), rbpg.isPhased());
}
}
genotypes.put(sample, pbtg);
// Update the cache
if (/*rbpg.isPhased() &&*/ rbpg.isHet()) {
rbpCache.put(sample, rbpg);
pbtCache.put(sample, pbtg);
} else if (!rbpg.isPhased()) {
rbpCache.remove(sample);
pbtCache.remove(sample);
}
}
}
VariantContext newvc = new VariantContext(SOURCE_NAME, pbt.getChr(), pbt.getStart(), pbt.getStart(), pbt.getAlleles(), genotypes, pbt.getNegLog10PError(), pbt.getFilters(), pbt.getAttributes());
vcfWriter.add(newvc);
}
}
return null;
}
@Override
public Integer reduceInit() {
return null;
}
@Override
public Integer reduce(Integer value, Integer sum) {
return null;
}
}

12
public/java/src/org/broadinstitute/sting/utils/Haplotype.java
View File

@ -33,8 +33,8 @@ import java.util.LinkedHashMap;
import java.util.List;
public class Haplotype {
protected byte[] bases = null;
protected double[] quals = null;
protected final byte[] bases;
protected final double[] quals;
private GenomeLoc genomeLocation = null;
private boolean isReference = false;
@ -69,6 +69,11 @@ public class Haplotype {
this.isReference = isRef;
}
@Override
public boolean equals( Object h ) {
return h instanceof Haplotype && Arrays.equals(bases, ((Haplotype) h).bases);
}
public double getQualitySum() {
double s = 0;
for (int k=0; k < bases.length; k++) {
@ -88,7 +93,7 @@ public class Haplotype {
public double[] getQuals() {
return quals;
}
public byte[] getBasesAsBytes() {
public byte[] getBases() {
return bases;
}
@ -100,7 +105,6 @@ public class Haplotype {
return genomeLocation.getStop();
}
public boolean isReference() {
return isReference;
}

23
public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java
View File

@ -1,10 +1,5 @@
package org.broadinstitute.sting.utils;
import com.google.java.contract.Ensures;
import com.google.java.contract.Invariant;
import com.google.java.contract.Requires;
import java.io.PrintStream;
/**
* A useful simple system for timing code. This code is not thread safe!
@ -13,11 +8,6 @@ import java.io.PrintStream;
* Date: Dec 10, 2010
* Time: 9:07:44 AM
*/
@Invariant({
"elapsed >= 0",
"startTime >= 0",
"name != null",
"! running || startTime > 0"})
public class SimpleTimer {
final private String name;
private long elapsed = 0l;
@ -27,7 +17,6 @@ public class SimpleTimer {
/**
* Creates an anonymous simple timer
*/
@Ensures("name != null && name.equals(\"Anonymous\")")
public SimpleTimer() {
this("Anonymous");
}
@ -36,8 +25,6 @@ public class SimpleTimer {
* Creates a simple timer named name
* @param name of the timer, must not be null
*/
@Requires("name != null")
@Ensures("this.name != null && this.name.equals(name)")
public SimpleTimer(String name) {
this.name = name;
}
@ -45,7 +32,6 @@ public class SimpleTimer {
/**
* @return the name associated with this timer
*/
@Ensures("result != null")
public synchronized String getName() {
return name;
}
@ -56,8 +42,6 @@ public class SimpleTimer {
*
* @return this object, for programming convenience
*/
@Requires("running == false")
@Ensures({"result != null", "elapsed == 0l"})
public synchronized SimpleTimer start() {
elapsed = 0l;
restart();
@ -71,8 +55,6 @@ public class SimpleTimer {
*
* @return this object, for programming convenience
*/
@Requires("running == false")
@Ensures("result != null")
public synchronized SimpleTimer restart() {
running = true;
startTime = currentTime();
@ -99,8 +81,6 @@ public class SimpleTimer {
*
* @return this object, for programming convenience
*/
@Requires("running == true")
@Ensures({"result != null", "elapsed >= old(elapsed)", "running == false"})
public synchronized SimpleTimer stop() {
running = false;
elapsed += currentTime() - startTime;
@ -113,9 +93,6 @@ public class SimpleTimer {
*
* @return this time, in seconds
*/
@Ensures({
"result >= (elapsed/1000.0)",
"result >= 0"})
public synchronized double getElapsedTime() {
return (running ? (currentTime() - startTime + elapsed) : elapsed) / 1000.0;
}

8
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -124,6 +124,14 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
executeTest("using expression", spec);
}
@Test
public void testUsingExpressionWithID() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --resource:foo " + validationDataLocation + "targetAnnotations.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.ID -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
Arrays.asList("4a6f0675242f685e9072c1da5ad9e715"));
executeTest("using expression with ID", spec);
}
@Test
public void testTabixAnnotations() {
final String MD5 = "13269d5a2e16f06fd755cc0fb9271acf";

28
public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java
View File

@ -1,28 +0,0 @@
package org.broadinstitute.sting.gatk.walkers.phasing;
import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.Test;
import java.util.Arrays;
public class MergeAndMatchHaplotypesIntegrationTest extends WalkerTest {
private static String mergeAndMatchHaplotypesTestDataRoot = validationDataLocation + "/MergeAndMatchHaplotypes";
private static String fundamentalTestPBTVCF = mergeAndMatchHaplotypesTestDataRoot + "/" + "FundamentalsTest.pbt.vcf";
private static String fundamentalTestRBPVCF = mergeAndMatchHaplotypesTestDataRoot + "/" + "FundamentalsTest.pbt.rbp.vcf";
@Test
public void testBasicFunctionality() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T MergeAndMatchHaplotypes",
"-R " + b37KGReference,
"--pbt " + fundamentalTestPBTVCF,
"--rbp " + fundamentalTestRBPVCF,
"-o %s"
),
1,
Arrays.asList("")
);
executeTest("testBasicMergeAndMatchHaplotypesFunctionality", spec);
}
}

6
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -9,7 +9,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
private static String variantEvalTestDataRoot = validationDataLocation + "VariantEval";
private static String fundamentalTestVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.snps_and_indels.vcf";
private static String fundamentalTestSNPsVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.vcf";
private static String fundamentalTestSNPsOneSampleVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.HG00625.vcf";
private static String fundamentalTestSNPsOneSampleVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.NA12045.vcf";
private static String cmdRoot = "-T VariantEval" +
" -R " + b36KGReference;
@ -359,7 +359,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testPerSampleAndSubsettedSampleHaveSameResults() {
String md5 = "b0565ac61b2860248e4abd478a177b5e";
String md5 = "7425ca5c439afd7bb33ed5cfea02c2b3";
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
@ -369,7 +369,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"--eval " + fundamentalTestSNPsVCF,
"-noEV",
"-EV CompOverlap",
"-sn HG00625",
"-sn NA12045",
"-noST",
"-L " + fundamentalTestSNPsVCF,
"-o %s"