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

This commit is contained in:
Eric Banks 2011-12-20 12:59:11 -05:00
parent 8ade2d6ac2 37e0044c48
commit 7204fcc2c3
14 changed files with 148 additions and 78 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationResult.java
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@ -48,8 +48,16 @@ public class AlleleFrequencyCalculationResult {
double log10LikelihoodOfAFzero = 0.0;
double log10PosteriorOfAFzero = 0.0;
AlleleFrequencyCalculationResult(int maxAltAlleles, int numChr) {
public AlleleFrequencyCalculationResult(int maxAltAlleles, int numChr) {
log10AlleleFrequencyLikelihoods = new double[maxAltAlleles][numChr+1];
log10AlleleFrequencyPosteriors = new double[maxAltAlleles][numChr+1];
}
public double getLog10LikelihoodOfAFzero() {
return log10LikelihoodOfAFzero;
}
public double getLog10PosteriorOfAFzero() {
return log10PosteriorOfAFzero;
}
}

6
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java
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@ -38,10 +38,10 @@ public abstract class FrequencyModeSelector implements Cloneable{
protected FrequencyModeSelector(GenomeLocParser parser) {
this.parser = parser;
}
protected void logCurrentSiteData(VariantContext vc, VariantContext subVC) {
logCurrentSiteData(vc, subVC, false, false);
protected void logCurrentSiteData(VariantContext vc, boolean passesCriteria) {
logCurrentSiteData(vc, passesCriteria, false, false);
}
protected abstract void logCurrentSiteData(VariantContext vc, VariantContext subVC, boolean IGNORE_GENOTYPES, boolean IGNORE_POLYMORPHIC);
protected abstract void logCurrentSiteData(VariantContext vc, boolean included, boolean IGNORE_GENOTYPES, boolean IGNORE_POLYMORPHIC);
protected abstract ArrayList<VariantContext> selectValidationSites(int numValidationSites);
}

43
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java
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@ -23,21 +23,52 @@
*/
package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector;
import org.broadinstitute.sting.gatk.walkers.genotyper.AlleleFrequencyCalculationResult;
import org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.TreeSet;
public class GLBasedSampleSelector extends SampleSelector {
public GLBasedSampleSelector(TreeSet<String> sm) {
Map<Integer,double[][]> numAllelePriorMatrix = new HashMap<Integer,double[][]>();
double referenceLikelihood;
public GLBasedSampleSelector(TreeSet<String> sm, double refLik) {
super(sm);
referenceLikelihood = refLik;
}
public VariantContext subsetSiteToSamples(VariantContext vc) {
/* todo - Look at sample array, and create a new vc with samples for which GL's indicate they should be included.
For example, include all samples (and corresponding genotypes) whose GL's are such that argmax(GL) = HET or HOMVAR. */
throw new ReviewedStingException("GLBasedSampleSelector not implemented yet!");
//return true;
public boolean selectSiteInSamples(VariantContext vc) {
if ( samples == null || samples.isEmpty() )
return true;
// want to include a site in the given samples if it is *likely* to be variant (via the EXACT model)
// first subset to the samples
VariantContext subContext = vc.subContextFromSamples(samples);
// now check to see (using EXACT model) whether this should be variant
// do we want to apply a prior? maybe user-spec?
double[][] flatPrior = createFlatPrior(vc.getAlleles());
AlleleFrequencyCalculationResult result = new AlleleFrequencyCalculationResult(vc.getAlternateAlleles().size(),2*samples.size());
ExactAFCalculationModel.linearExactMultiAllelic(subContext.getGenotypes(),vc.getAlternateAlleles().size(),flatPrior,result,true);
// do we want to let this qual go up or down?
if ( result.getLog10PosteriorOfAFzero() < referenceLikelihood ) {
return true;
}
return false;
}
private double[][] createFlatPrior(List<Allele> alleles) {
if ( ! numAllelePriorMatrix.containsKey(alleles.size()) ) {
numAllelePriorMatrix.put(alleles.size(), new double[alleles.size()][1+2*samples.size()]);
}
return numAllelePriorMatrix.get(alleles.size());
}
}

10
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java
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@ -38,14 +38,18 @@ public class GTBasedSampleSelector extends SampleSelector{
super(sm);
}
public VariantContext subsetSiteToSamples(VariantContext vc) {
public boolean selectSiteInSamples(VariantContext vc) {
// Super class already defined initialization which filled data structure "samples" with desired samples.
// We only need to check if current vc if polymorphic in that set of samples
if ( samples == null || samples.isEmpty() )
return vc;
return true;
return vc.subContextFromSamples(samples, vc.getAlleles());
VariantContext subContext = vc.subContextFromSamples(samples, vc.getAlleles());
if ( subContext.isPolymorphicInSamples() ) {
return true;
}
return false;
}
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java
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@ -60,7 +60,7 @@ public class KeepAFSpectrumFrequencySelector extends FrequencyModeSelector {
postSampleSelectionHistogram = new int[NUM_BINS];
}
public void logCurrentSiteData(VariantContext vc, VariantContext subVC, boolean IGNORE_GENOTYPES, boolean IGNORE_POLYMORPHIC) {
public void logCurrentSiteData(VariantContext vc, boolean selectedInTargetSamples, boolean IGNORE_GENOTYPES, boolean IGNORE_POLYMORPHIC) {
// this method is called for every variant of a selected type, regardless of whether it will be selectable or not
// get AC,AF,AN attributes from vc
@ -107,7 +107,7 @@ public class KeepAFSpectrumFrequencySelector extends FrequencyModeSelector {
numTotalSites++;
// now process VC subsetted to samples of interest
if (!subVC.isPolymorphicInSamples() && !IGNORE_POLYMORPHIC)
if (! selectedInTargetSamples && !IGNORE_POLYMORPHIC)
return;
//System.out.format("Post:%4.4f %d\n",af0, binIndex);

5
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java
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@ -33,8 +33,7 @@ public class NullSampleSelector extends SampleSelector{
super(sm);
}
public VariantContext subsetSiteToSamples(VariantContext vc) {
return vc;
public boolean selectSiteInSamples(VariantContext vc) {
return true;
}
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java
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@ -34,7 +34,7 @@ public abstract class SampleSelector implements Cloneable {
samples = new TreeSet<String>(sm);
}
protected abstract VariantContext subsetSiteToSamples(VariantContext vc);
protected abstract boolean selectSiteInSamples(VariantContext vc);
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java
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@ -42,14 +42,14 @@ public class UniformSamplingFrequencySelector extends FrequencyModeSelector {
}
public void logCurrentSiteData(VariantContext vc, VariantContext subVC, boolean IGNORE_GENOTYPES, boolean IGNORE_POLYMORPHIC) {
public void logCurrentSiteData(VariantContext vc, boolean selectedInTargetSamples, boolean IGNORE_GENOTYPES, boolean IGNORE_POLYMORPHIC) {
HashMap<String, Object> attributes = new HashMap<String, Object>();
if (vc.hasGenotypes() && !IGNORE_GENOTYPES) {
// recompute AF,AC,AN based on genotypes:
VariantContextUtils.calculateChromosomeCounts(vc, attributes, false);
if (!subVC.isPolymorphicInSamples() && !IGNORE_POLYMORPHIC)
if (! selectedInTargetSamples && !IGNORE_POLYMORPHIC)
return;
} else {
if ( attributes.containsKey(VCFConstants.ALLELE_COUNT_KEY) ) {

17
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelectorWalker.java
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@ -124,6 +124,10 @@ public class ValidationSiteSelectorWalker extends RodWalker<Integer, Integer> {
@Argument(fullName="sampleMode", shortName="sampleMode", doc="Sample selection mode", required=false)
private SAMPLE_SELECTION_MODE sampleMode = SAMPLE_SELECTION_MODE.NONE;
@Argument(shortName="samplePNonref",fullName="samplePNonref", doc="GL-based selection mode only: the probability" +
" that a site is non-reference in the samples for which to include the site",required=false)
private double samplePNonref = 0.99;
@Argument(fullName="numValidationSites", shortName="numSites", doc="Number of output validation sites", required=true)
private int numValidationSites;
@ -231,13 +235,14 @@ public class ValidationSiteSelectorWalker extends RodWalker<Integer, Integer> {
continue;
// do anything required by frequency selector before we select for samples
VariantContext subVC;
// does this site pass the criteria for the samples we are interested in?
boolean passesSampleSelectionCriteria;
if (samples.isEmpty())
subVC = vc;
passesSampleSelectionCriteria = true;
else
subVC = sampleSelector.subsetSiteToSamples(vc);
frequencyModeSelector.logCurrentSiteData(vc, subVC, IGNORE_GENOTYPES, IGNORE_POLYMORPHIC);
passesSampleSelectionCriteria = sampleSelector.selectSiteInSamples(vc);
frequencyModeSelector.logCurrentSiteData(vc,passesSampleSelectionCriteria,IGNORE_GENOTYPES,IGNORE_POLYMORPHIC);
}
return 1;
}
@ -263,7 +268,7 @@ public class ValidationSiteSelectorWalker extends RodWalker<Integer, Integer> {
SampleSelector sm;
switch ( sampleMode ) {
case POLY_BASED_ON_GL:
sm = new GLBasedSampleSelector(samples);
sm = new GLBasedSampleSelector(samples, Math.log10(1.0-samplePNonref));
break;
case POLY_BASED_ON_GT:
sm = new GTBasedSampleSelector(samples);

38
public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java
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@ -104,6 +104,10 @@ public class ClippingOp {
break;
case REVERT_SOFTCLIPPED_BASES:
read = revertSoftClippedBases(read);
break;
default:
throw new IllegalStateException("Unexpected Clipping operator type " + algorithm);
}
@ -111,6 +115,38 @@ public class ClippingOp {
return read;
}
private GATKSAMRecord revertSoftClippedBases(GATKSAMRecord read) {
GATKSAMRecord unclipped;
// shallow copy of the read bases and quals should be fine here because they are immutable in the original read
try {
unclipped = (GATKSAMRecord) read.clone();
} catch (CloneNotSupportedException e) {
throw new ReviewedStingException("Where did the clone go?");
}
Cigar unclippedCigar = new Cigar();
int matchesCount = 0;
for (CigarElement element : read.getCigar().getCigarElements()) {
if (element.getOperator() == CigarOperator.SOFT_CLIP || element.getOperator() == CigarOperator.MATCH_OR_MISMATCH)
matchesCount += element.getLength();
else if (matchesCount > 0) {
unclippedCigar.add(new CigarElement(matchesCount, CigarOperator.MATCH_OR_MISMATCH));
matchesCount = 0;
unclippedCigar.add(element);
}
else
unclippedCigar.add(element);
}
if (matchesCount > 0)
unclippedCigar.add(new CigarElement(matchesCount, CigarOperator.MATCH_OR_MISMATCH));
unclipped.setCigar(unclippedCigar);
unclipped.setAlignmentStart(read.getAlignmentStart() + calculateAlignmentStartShift(read.getCigar(), unclippedCigar));
return unclipped;
}
/**
* Given a cigar string, get the number of bases hard or soft clipped at the start
*/
@ -472,7 +508,7 @@ public class ClippingOp {
for (CigarElement cigarElement : oldCigar.getCigarElements()) {
if (cigarElement.getOperator() == CigarOperator.HARD_CLIP || cigarElement.getOperator() == CigarOperator.SOFT_CLIP )
oldShift += Math.min(cigarElement.getLength(), newShift - oldShift);
oldShift += cigarElement.getLength();
else if (readHasStarted)
break;
}

7
public/java/src/org/broadinstitute/sting/utils/clipping/ClippingRepresentation.java
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@ -29,5 +29,10 @@ public enum ClippingRepresentation {
* lossy) operation. Note that this can only be applied to cases where the clipped
* bases occur at the start or end of a read.
*/
HARDCLIP_BASES
HARDCLIP_BASES,
/**
* Turn all soft-clipped bases into matches
*/
REVERT_SOFTCLIPPED_BASES,
}

5
public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java
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@ -213,4 +213,9 @@ public class ReadClipper {
}
return clipRead(ClippingRepresentation.HARDCLIP_BASES);
}
public GATKSAMRecord revertSoftClippedBases() {
this.addOp(new ClippingOp(0, 0)); // UNSOFTCLIP_BASES doesn't need coordinates
return this.clipRead(ClippingRepresentation.REVERT_SOFTCLIPPED_BASES);
}
}

44
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -851,50 +851,6 @@ public class ReadUtils {
return new Pair<Integer, Boolean>(readBases, fallsInsideDeletion);
}
public static GATKSAMRecord unclipSoftClippedBases(GATKSAMRecord read) {
int newReadStart = read.getAlignmentStart();
int newReadEnd = read.getAlignmentEnd();
List<CigarElement> newCigarElements = new ArrayList<CigarElement>(read.getCigar().getCigarElements().size());
int heldOver = -1;
boolean sSeen = false;
for ( CigarElement e : read.getCigar().getCigarElements() ) {
if ( e.getOperator().equals(CigarOperator.S) ) {
newCigarElements.add(new CigarElement(e.getLength(),CigarOperator.M));
if ( sSeen ) {
newReadEnd += e.getLength();
sSeen = true;
} else {
newReadStart -= e.getLength();
}
} else {
newCigarElements.add(e);
}
}
// merge duplicate operators together
int idx = 0;
List<CigarElement> finalCigarElements = new ArrayList<CigarElement>(read.getCigar().getCigarElements().size());
while ( idx < newCigarElements.size() -1 ) {
if ( newCigarElements.get(idx).getOperator().equals(newCigarElements.get(idx+1).getOperator()) ) {
int combSize = newCigarElements.get(idx).getLength();
int offset = 0;
while ( idx + offset < newCigarElements.size()-1 && newCigarElements.get(idx+offset).getOperator().equals(newCigarElements.get(idx+1+offset).getOperator()) ) {
combSize += newCigarElements.get(idx+offset+1).getLength();
offset++;
}
finalCigarElements.add(new CigarElement(combSize,newCigarElements.get(idx).getOperator()));
idx = idx + offset -1;
} else {
finalCigarElements.add(newCigarElements.get(idx));
}
idx++;
}
read.setCigar(new Cigar(finalCigarElements));
read.setAlignmentStart(newReadStart);
return read;
}
/**
* Compares two SAMRecords only the basis on alignment start. Note that
* comparisons are performed ONLY on the basis of alignment start; any

31
public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java
View File

@ -279,9 +279,9 @@ public class ReadClipperUnitTest extends BaseTest {
GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
GATKSAMRecord clippedRead = (new ReadClipper(read)).hardClipLeadingInsertions();
int expectedLength = read.getReadLength() - leadingInsertionLength(read.getCigar());
int expectedLength = read.getReadLength() - leadingCigarElementLength(read.getCigar(), CigarOperator.INSERTION);
if (cigarHasElementsDifferentThanInsertionsAndHardClips(read.getCigar()))
expectedLength -= leadingInsertionLength(ReadClipperTestUtils.invertCigar(read.getCigar()));
expectedLength -= leadingCigarElementLength(ReadClipperTestUtils.invertCigar(read.getCigar()), CigarOperator.INSERTION);
if (! clippedRead.isEmpty()) {
Assert.assertEquals(expectedLength, clippedRead.getReadLength(), String.format("%s -> %s", read.getCigarString(), clippedRead.getCigarString())); // check that everything else is still there
@ -293,6 +293,27 @@ public class ReadClipperUnitTest extends BaseTest {
}
}
@Test(enabled = true)
public void testRevertSoftClippedBases()
{
for (Cigar cigar: cigarList) {
final int leadingSoftClips = leadingCigarElementLength(cigar, CigarOperator.SOFT_CLIP);
final int tailSoftClips = leadingCigarElementLength(ReadClipperTestUtils.invertCigar(cigar), CigarOperator.SOFT_CLIP);
final GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
final GATKSAMRecord unclipped = (new ReadClipper(read)).revertSoftClippedBases();
if ( leadingSoftClips > 0 || tailSoftClips > 0) {
final int expectedStart = read.getAlignmentStart() - leadingSoftClips;
final int expectedEnd = read.getAlignmentEnd() + tailSoftClips;
Assert.assertEquals(unclipped.getAlignmentStart(), expectedStart);
Assert.assertEquals(unclipped.getAlignmentEnd(), expectedEnd);
}
else
Assert.assertEquals(read.getCigarString(), unclipped.getCigarString());
}
}
private void assertNoLowQualBases(GATKSAMRecord read, byte low_qual) {
@ -304,12 +325,12 @@ public class ReadClipperUnitTest extends BaseTest {
}
private boolean startsWithInsertion(Cigar cigar) {
return leadingInsertionLength(cigar) > 0;
return leadingCigarElementLength(cigar, CigarOperator.INSERTION) > 0;
}
private int leadingInsertionLength(Cigar cigar) {
private int leadingCigarElementLength(Cigar cigar, CigarOperator operator) {
for (CigarElement cigarElement : cigar.getCigarElements()) {
if (cigarElement.getOperator() == CigarOperator.INSERTION)
if (cigarElement.getOperator() == operator)
return cigarElement.getLength();
if (cigarElement.getOperator() != CigarOperator.HARD_CLIP)
break;