zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
View File

@ -242,7 +242,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
return new PhasingStatsAndOutput(phaseStats, completedList); 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) { private VariantContext reduceVCToSamples(VariantContext vc, List<String> samplesToPhase) {
// for ( String sample : samplesToPhase ) // for ( String sample : samplesToPhase )