diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java index 1c372aa82..b1720e509 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java @@ -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(); 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 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 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);