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Now that Mauricio has updated the PacBio BAM to properly have RG, can use sample name in the walker 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5212 348d0f76-0448-11de-a6fe-93d51630548a
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fromer 2011-02-07 20:26:57 +00:00
parent ecbc38aff0
commit bceb2a9460
1 changed files with 0 additions and 6 deletions
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6
java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBasedPhasingValidationWalker.java
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@ -144,10 +144,6 @@ public class ReadBasedPhasingValidationWalker extends RodWalker<Integer, Integer
ReadBackedPileup pileup = context.getBasePileup(); ReadBackedPileup pileup = context.getBasePileup();
String nextName = null; String nextName = null;
//
// TODO: ASSUMES THAT ALL READS COME FROM A SINGLE SAMPLE:
// TODO: CODE SHOULD BE AS FOLLOWS:
/*
Collection<String> sampNames = pileup.getSampleNames(); Collection<String> sampNames = pileup.getSampleNames();
if (sampNames.size() != 1) if (sampNames.size() != 1)
throw new UserException("Reads must be for exactly one sample [not multi-sample]"); throw new UserException("Reads must be for exactly one sample [not multi-sample]");
@ -161,8 +157,6 @@ public class ReadBasedPhasingValidationWalker extends RodWalker<Integer, Integer
throw new UserException("Reads must have a single consistent sample name"); throw new UserException("Reads must have a single consistent sample name");
pileup = pileup.getPileupForSampleName(sampleName); pileup = pileup.getPileupForSampleName(sampleName);
*/
//
ReadBasesAtPosition readBases = new ReadBasesAtPosition(); ReadBasesAtPosition readBases = new ReadBasesAtPosition();
for (PileupElement p : pileup) for (PileupElement p : pileup)