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Final checkpoint: all tests pass. Note that there were bugs in the PoolGenotypeLikelihoodsUnitTest that needed fixing and eventually led to my needing to disable one of the tests (with a note for Guillermo to look into it). Also note that while I have moved over the GATK to use the new non-null representation of Alleles, I didn't remove all of the now-superfluous code throughout to do padding checking on merges; we'll need to do this on a subsequent push.

This commit is contained in:
Eric Banks 2012-07-29 01:07:59 -04:00
parent 2b1b00ade5
commit 99b15b2b3a
4 changed files with 93 additions and 112 deletions
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24
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypeLikelihoodsUnitTest.java
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@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import net.sf.samtools.SAMUtils;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
@ -290,15 +289,17 @@ public class PoolGenotypeLikelihoodsUnitTest {
}
@Test
// TODO -- Guillermo, this test cannot work because the ArtificialReadPileupTestProvider returns a position of chr1:5, which is less than
// TODO -- HAPLOTYPE_SIZE in IndelGenotypeLikelihoodsCalculationModel.getHaplotypeMapFromAlleles() so the HaplotypeMap is not populated.
@Test (enabled = false)
public void testIndelErrorModel() {
final ArtificialReadPileupTestProvider refPileupTestProvider = new ArtificialReadPileupTestProvider(1,"ref");
final byte refByte = refPileupTestProvider.getRefByte();
final String altBases = refByte + "TCA";
final String altBases = (char)refByte + "TCA";
final String refSampleName = refPileupTestProvider.getSampleNames().get(0);
final List<Allele> trueAlleles = new ArrayList<Allele>();
trueAlleles.add(Allele.create(refByte, true));
trueAlleles.add(Allele.create(refByte + "TC", false));
trueAlleles.add(Allele.create((char)refByte + "TC", false));
final String fw = new String(refPileupTestProvider.getReferenceContext().getForwardBases());
final VariantContext refInsertionVC = new VariantContextBuilder("test","chr1",refPileupTestProvider.getReferenceContext().getLocus().getStart(),
@ -392,9 +393,6 @@ public class PoolGenotypeLikelihoodsUnitTest {
final byte refByte = readPileupTestProvider.getRefByte();
final byte altByte = refByte == (byte)'T'? (byte) 'C': (byte)'T';
final int refIdx = BaseUtils.simpleBaseToBaseIndex(refByte);
final int altIdx = BaseUtils.simpleBaseToBaseIndex(altByte);
final List<Allele> allAlleles = new ArrayList<Allele>(); // this contains only ref Allele up to now
final Set<String> laneIDs = new TreeSet<String>();
laneIDs.add(GenotypeLikelihoodsCalculationModel.DUMMY_LANE);
@ -411,11 +409,17 @@ public class PoolGenotypeLikelihoodsUnitTest {
for (String laneID : laneIDs)
noisyErrorModels.put(laneID, Q30ErrorModel);
final int refIdx = 0;
int altIdx = 2;
// ref allele must be first
allAlleles.add(Allele.create(refByte, true));
for (byte b: BaseUtils.BASES) {
if (refByte == b)
allAlleles.add(Allele.create(b,true));
else
if (refByte != b) {
if (b == altByte)
altIdx = allAlleles.size();
allAlleles.add(Allele.create(b, false));
}
}
PrintStream out = null;

143
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java
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@ -38,9 +38,6 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
import java.util.*;
@ -103,39 +100,27 @@ public class ArtificialReadPileupTestProvider {
boolean addBaseErrors, int phredScaledBaseErrorRate) {
// RefMetaDataTracker tracker = new RefMetaDataTracker(null,referenceContext);
ArrayList<Allele> vcAlleles = new ArrayList<Allele>();
String refBase = refBases.substring(offset,offset+1); // referenceContext.getBase()?
Allele refAllele, altAllele;
String refAllele, altAllele;
if (eventLength == 0) {
// SNP case
refAllele = Allele.create(refBase,true);
altAllele = Allele.create(altBases.substring(0,1), false);
refAllele = new String(new byte[]{referenceContext.getBase()});
altAllele = new String(altBases.substring(0,1));
} else if (eventLength>0){
// insertion
refAllele = Allele.create(refBase,true);
altAllele = Allele.create(refBase + altBases.substring(0,eventLength), false);
refAllele = "";
altAllele = altBases.substring(0,eventLength);
}
else {
// deletion
refAllele = Allele.create(refBases.substring(offset,offset+Math.abs(eventLength)),true);
altAllele = Allele.create(refBase, false);
refAllele = refBases.substring(offset,offset+Math.abs(eventLength));
altAllele = "";
}
int stop = loc.getStart();
vcAlleles.add(refAllele);
vcAlleles.add(altAllele);
final VariantContextBuilder builder = new VariantContextBuilder().source("");
builder.loc(loc.getContig(), loc.getStart(), stop);
builder.alleles(vcAlleles);
builder.noGenotypes();
final VariantContext vc = builder.make();
Map<String,AlignmentContext> contexts = new HashMap<String,AlignmentContext>();
for (String sample: sampleNames) {
AlignmentContext context = new AlignmentContext(loc, generateRBPForVariant(loc,vc, altBases, numReadsPerAllele, sample, addBaseErrors, phredScaledBaseErrorRate));
AlignmentContext context = new AlignmentContext(loc, generateRBPForVariant(loc, refAllele, altAllele, altBases, numReadsPerAllele, sample, addBaseErrors, phredScaledBaseErrorRate));
contexts.put(sample,context);
}
@ -149,73 +134,71 @@ public class ArtificialReadPileupTestProvider {
rg.setSample(name);
return rg;
}
private ReadBackedPileup generateRBPForVariant( GenomeLoc loc, VariantContext vc, String altBases,
private ReadBackedPileup generateRBPForVariant( GenomeLoc loc, String refAllele, String altAllele, String altBases,
int[] numReadsPerAllele, String sample, boolean addErrors, int phredScaledErrorRate) {
List<PileupElement> pileupElements = new ArrayList<PileupElement>();
int readStart = contigStart;
int offset = (contigStop-contigStart+1)/2;
int refAlleleLength = 0;
int readCounter = 0;
int alleleCounter = 0;
for (Allele allele: vc.getAlleles()) {
if (allele.isReference())
refAlleleLength = allele.getBases().length;
int alleleLength = allele.getBases().length;
for ( int d = 0; d < numReadsPerAllele[alleleCounter]; d++ ) {
byte[] readBases = trueHaplotype(allele, offset, refAlleleLength);
if (addErrors)
addBaseErrors(readBases, phredScaledErrorRate);
byte[] readQuals = new byte[readBases.length];
Arrays.fill(readQuals, (byte)phredScaledErrorRate);
GATKSAMRecord read = new GATKSAMRecord(header);
read.setBaseQualities(readQuals);
read.setReadBases(readBases);
read.setReadName(artificialReadName+readCounter++);
boolean isBeforeDeletion = false, isBeforeInsertion = false;
if (allele.isReference())
read.setCigarString(readBases.length + "M");
else {
isBeforeDeletion = alleleLength<refAlleleLength;
isBeforeInsertion = alleleLength>refAlleleLength;
if (isBeforeDeletion || isBeforeInsertion)
read.setCigarString(offset+"M"+ alleleLength + (isBeforeDeletion?"D":"I") +
(readBases.length-offset)+"M");
else // SNP case
read.setCigarString(readBases.length+"M");
}
int eventLength = (isBeforeDeletion?refAlleleLength:(isBeforeInsertion?alleleLength:0));
read.setReadPairedFlag(false);
read.setAlignmentStart(readStart);
read.setMappingQuality(artificialMappingQuality);
read.setReferenceName(loc.getContig());
read.setReadNegativeStrandFlag(false);
read.setAttribute("RG", sampleRG(sample).getReadGroupId());
pileupElements.add(new PileupElement(read,offset,false,isBeforeDeletion, false, isBeforeInsertion,false,false,altBases.substring(0,alleleLength),eventLength));
}
alleleCounter++;
}
int refAlleleLength = refAllele.length();
pileupElements.addAll(createPileupElements(refAllele, loc, numReadsPerAllele[0], sample, contigStart, offset, altBases, addErrors, phredScaledErrorRate, refAlleleLength, true));
pileupElements.addAll(createPileupElements(altAllele, loc, numReadsPerAllele[1], sample, contigStart, offset, altBases, addErrors, phredScaledErrorRate, refAlleleLength, false));
return new ReadBackedPileupImpl(loc,pileupElements);
}
private byte[] trueHaplotype(Allele allele, int offset, int refAlleleLength) {
private List<PileupElement> createPileupElements(String allele, GenomeLoc loc, int numReadsPerAllele, String sample, int readStart, int offset, String altBases, boolean addErrors, int phredScaledErrorRate, int refAlleleLength, boolean isReference) {
int alleleLength = allele.length();
List<PileupElement> pileupElements = new ArrayList<PileupElement>();
int readCounter = 0;
for ( int d = 0; d < numReadsPerAllele; d++ ) {
byte[] readBases = trueHaplotype(allele, offset, refAlleleLength);
if (addErrors)
addBaseErrors(readBases, phredScaledErrorRate);
byte[] readQuals = new byte[readBases.length];
Arrays.fill(readQuals, (byte)phredScaledErrorRate);
GATKSAMRecord read = new GATKSAMRecord(header);
read.setBaseQualities(readQuals);
read.setReadBases(readBases);
read.setReadName(artificialReadName+readCounter++);
boolean isBeforeDeletion = false, isBeforeInsertion = false;
if (isReference)
read.setCigarString(readBases.length + "M");
else {
isBeforeDeletion = alleleLength<refAlleleLength;
isBeforeInsertion = alleleLength>refAlleleLength;
if (isBeforeDeletion || isBeforeInsertion)
read.setCigarString(offset+"M"+ alleleLength + (isBeforeDeletion?"D":"I") +
(readBases.length-offset)+"M");
else // SNP case
read.setCigarString(readBases.length+"M");
}
int eventLength = (isBeforeDeletion?refAlleleLength:(isBeforeInsertion?alleleLength:0));
read.setReadPairedFlag(false);
read.setAlignmentStart(readStart);
read.setMappingQuality(artificialMappingQuality);
read.setReferenceName(loc.getContig());
read.setReadNegativeStrandFlag(false);
read.setAttribute("RG", sampleRG(sample).getReadGroupId());
pileupElements.add(new PileupElement(read,offset,false,isBeforeDeletion, false, isBeforeInsertion,false,false,altBases.substring(0,alleleLength),eventLength));
}
return pileupElements;
}
private byte[] trueHaplotype(String allele, int offset, int refAlleleLength) {
// create haplotype based on a particular allele
String prefix = refBases.substring(offset);
String alleleBases = new String(allele.getBases());
String prefix = refBases.substring(0, offset);
String postfix = refBases.substring(offset+refAlleleLength,refBases.length());
return (prefix+alleleBases+postfix).getBytes();
return (prefix+allele+postfix).getBytes();
}
private void addBaseErrors(final byte[] readBases, final int phredScaledErrorRate) {

6
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java
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@ -70,7 +70,7 @@ public class IndelGenotypeLikelihoodsUnitTest extends BaseTest {
List<Allele> alleles = getConsensusAlleles(eventLength,true,10,0.1, altBases);
Assert.assertEquals(alleles.size(),2);
Assert.assertEquals(alleles.get(1).getBaseString(), altBases.substring(0,eventLength));
Assert.assertEquals(alleles.get(1).getBaseString().substring(1), altBases.substring(0,eventLength));
@ -79,7 +79,7 @@ public class IndelGenotypeLikelihoodsUnitTest extends BaseTest {
eventLength = 3;
alleles = getConsensusAlleles(eventLength,false,10,0.1, altBases);
Assert.assertEquals(alleles.size(),2);
Assert.assertEquals(alleles.get(0).getBaseString(), refBases.substring(pileupProvider.offset,pileupProvider.offset+eventLength));
Assert.assertEquals(alleles.get(0).getBaseString().substring(1), refBases.substring(pileupProvider.offset,pileupProvider.offset+eventLength));
// same with min Reads = 11
alleles = getConsensusAlleles(eventLength,false,11,0.1, altBases);
@ -97,7 +97,7 @@ public class IndelGenotypeLikelihoodsUnitTest extends BaseTest {
alleles = getConsensusAlleles(eventLength,true,10,0.1, altBases);
Assert.assertEquals(alleles.size(),2);
Assert.assertEquals(alleles.get(1).getBaseString(), altBases.substring(0,eventLength));
Assert.assertEquals(alleles.get(1).getBaseString().substring(1), altBases.substring(0,eventLength));
altBases = "CCTCNTGAGA";
eventLength = 5;

32
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
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@ -39,7 +39,7 @@ import java.io.FileNotFoundException;
import java.util.*;
public class VariantContextUtilsUnitTest extends BaseTest {
Allele Aref, T, C, delRef, Cref, ATC, ATCATC;
Allele Aref, T, C, Cref, ATC, ATCATC;
private GenomeLocParser genomeLocParser;
@BeforeSuite
@ -56,7 +56,6 @@ public class VariantContextUtilsUnitTest extends BaseTest {
// alleles
Aref = Allele.create("A", true);
Cref = Allele.create("C", true);
delRef = Allele.create("-", true);
T = Allele.create("T");
C = Allele.create("C");
ATC = Allele.create("ATC");
@ -156,28 +155,23 @@ public class VariantContextUtilsUnitTest extends BaseTest {
Arrays.asList(Aref, C),
Arrays.asList(Aref, T, C)); // in order of appearence
// The following is actually a pathological case - there's no way on a vcf to represent a null allele that's non-variant.
// The code converts this (correctly) to a single-base non-variant vc with whatever base was there as a reference.
new MergeAllelesTest(Arrays.asList(delRef),
Arrays.asList(Cref));
new MergeAllelesTest(Arrays.asList(Aref),
Arrays.asList(Aref, ATC),
Arrays.asList(Aref, ATC));
new MergeAllelesTest(Arrays.asList(delRef),
Arrays.asList(delRef, ATC),
Arrays.asList(delRef, ATC));
new MergeAllelesTest(Arrays.asList(delRef),
Arrays.asList(delRef, ATC, ATCATC),
Arrays.asList(delRef, ATC, ATCATC));
new MergeAllelesTest(Arrays.asList(Aref),
Arrays.asList(Aref, ATC, ATCATC),
Arrays.asList(Aref, ATC, ATCATC));
// alleles in the order we see them
new MergeAllelesTest(Arrays.asList(delRef, ATCATC),
Arrays.asList(delRef, ATC, ATCATC),
Arrays.asList(delRef, ATCATC, ATC));
new MergeAllelesTest(Arrays.asList(Aref, ATCATC),
Arrays.asList(Aref, ATC, ATCATC),
Arrays.asList(Aref, ATCATC, ATC));
// same
new MergeAllelesTest(Arrays.asList(delRef, ATC),
Arrays.asList(delRef, ATCATC),
Arrays.asList(delRef, ATC, ATCATC));
new MergeAllelesTest(Arrays.asList(Aref, ATC),
Arrays.asList(Aref, ATCATC),
Arrays.asList(Aref, ATC, ATCATC));
return MergeAllelesTest.getTests(MergeAllelesTest.class);
}