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Walker to perform deterministic annotation of phasing by transmission (to be compatible with RBP's definition of consecutive pairwise phasing)

This commit is contained in:
Menachem Fromer 2011-07-15 17:44:31 -04:00
parent ce4d702e25
commit 72f4cf9c0e
1 changed files with 1 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
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@ -242,7 +242,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
return new PhasingStatsAndOutput(phaseStats, completedList);
}
private static final Set<String> KEYS_TO_KEEP_IN_REDUCED_VCF = new HashSet<String>(Arrays.asList("PQ"));
private static final Set<String> KEYS_TO_KEEP_IN_REDUCED_VCF = new HashSet<String>(Arrays.asList(PQ_KEY));
private VariantContext reduceVCToSamples(VariantContext vc, List<String> samplesToPhase) {
// for ( String sample : samplesToPhase )