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Exhaustive unit tests for Pool SNP genotype likelihoods: 

a) Add ability for ErrorModel to be specified by external log-probability vector for testing.
b) For a given depth and ploidy(=2*samples/pool), create artificial high quality pileup testing from AC=0 to AC=ploidy, and test that pool GL's have expected content.Misc. refactorings and cleanups
c) Misc. cleanups and beautification.
This commit is contained in:
Guillermo del Angel 2012-04-30 14:29:46 -04:00
parent 7d029b9a28
commit e185632013
1 changed files with 10 additions and 2 deletions
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12
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java
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@ -65,8 +65,9 @@ public class ArtificialReadPileupTestProvider {
public final GenomeLoc window = genomeLocParser.createGenomeLoc(artificialContig,artificialRefStart,10);
public final ReferenceContext referenceContext = new ReferenceContext(genomeLocParser,loc,window,this.refBases.getBytes());
byte BASE_QUAL = 50;
public ArtificialReadPileupTestProvider(int numSamples, final String SAMPLE_PREFIX) {
public ArtificialReadPileupTestProvider(final int numSamples, final String SAMPLE_PREFIX) {
sampleRGs = new ArrayList<SAMReadGroupRecord>();
for ( int i = 0; i < numSamples; i++ ) {
@ -78,6 +79,10 @@ public class ArtificialReadPileupTestProvider {
}
public ArtificialReadPileupTestProvider(final int numSamples, final String SAMPLE_PREFIX, final byte q) {
this(numSamples,SAMPLE_PREFIX);
BASE_QUAL = q;
}
public List<String> getSampleNames() {
return sampleNames;
}
@ -85,6 +90,9 @@ public class ArtificialReadPileupTestProvider {
return refBases.substring(offset,offset+1).getBytes()[0];
}
public ReferenceContext getReferenceContext() { return referenceContext;}
public GenomeLocParser getGenomeLocParser() { return genomeLocParser; }
public Map<String,AlignmentContext> getAlignmentContextFromAlleles(int eventLength, String altBases, int[] numReadsPerAllele) {
// RefMetaDataTracker tracker = new RefMetaDataTracker(null,referenceContext);
@ -151,7 +159,7 @@ public class ArtificialReadPileupTestProvider {
for ( int d = 0; d < numReadsPerAllele[alleleCounter]; d++ ) {
byte[] readBases = trueHaplotype(allele, offset, refAlleleLength);
byte[] readQuals = new byte[readBases.length];
Arrays.fill(readQuals, (byte) 50);
Arrays.fill(readQuals, (byte)BASE_QUAL);
GATKSAMRecord read = new GATKSAMRecord(header);
read.setBaseQualities(readQuals);