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 e48c4d197..39b81f4a2 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 @@ -37,6 +37,7 @@ import org.broadinstitute.sting.utils.pileup.PileupElement; 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.GATKSAMReadGroupRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import java.util.*; @@ -53,11 +54,11 @@ public class ArtificialReadPileupTestProvider { final String artificialReadName = "synth"; final int artificialRefStart = 1; final int artificialMappingQuality = 60; - Map sample2RG = new HashMap(); + Map sample2RG = new HashMap(); List sampleRGs; List sampleNames = new ArrayList(); private String sampleName(int i) { return sampleNames.get(i); } - private SAMReadGroupRecord sampleRG(String name) { return sample2RG.get(name); } + private GATKSAMReadGroupRecord sampleRG(String name) { return sample2RG.get(name); } public final int locStart = 105; // start position where we desire artificial variant private final int readLength = 10; // desired read length in pileup public final int readOffset = 4; @@ -75,7 +76,7 @@ public class ArtificialReadPileupTestProvider { for ( int i = 0; i < numSamples; i++ ) { sampleNames.add(String.format("%s%04d", SAMPLE_PREFIX, i)); - SAMReadGroupRecord rg = createRG(sampleName(i)); + GATKSAMReadGroupRecord rg = createRG(sampleName(i)); sampleRGs.add(rg); sample2RG.put(sampleName(i), rg); } @@ -134,8 +135,8 @@ public class ArtificialReadPileupTestProvider { return contexts; } - private SAMReadGroupRecord createRG(String name) { - SAMReadGroupRecord rg = new SAMReadGroupRecord(name); + private GATKSAMReadGroupRecord createRG(String name) { + GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(name); rg.setPlatform("ILLUMINA"); rg.setSample(name); return rg; @@ -189,7 +190,7 @@ public class ArtificialReadPileupTestProvider { read.setMappingQuality(artificialMappingQuality); read.setReferenceName(loc.getContig()); read.setReadNegativeStrandFlag(false); - read.setAttribute("RG", sampleRG(sample).getReadGroupId()); + read.setReadGroup(sampleRG(sample)); pileupElements.add(new PileupElement(read,readOffset,false,isBeforeDeletion, false, isBeforeInsertion,false,false,altBases,Math.abs(eventLength)));