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VC utils prune method now will keep genotype attributes as well as info keys. RBP now emits a far reduce (NO INFO, only GT:GQ:PG) records, further reducing size of phasing output 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4882 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-12-20 16:33:14 +00:00
parent 8604335566
commit 60880b925f
2 changed files with 7 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
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@ -293,6 +293,7 @@ public class VariantContextUtils {
Map<String, Object> d = mvc.getAttributes(); Map<String, Object> d = mvc.getAttributes();
mvc.clearAttributes(); mvc.clearAttributes();
for ( String key : keysToPreserve ) for ( String key : keysToPreserve )
if ( d.containsKey(key) )
mvc.putAttribute(key, d.get(key)); mvc.putAttribute(key, d.get(key));
} }
@ -301,6 +302,9 @@ public class VariantContextUtils {
for ( Genotype g : gs ) { for ( Genotype g : gs ) {
MutableGenotype mg = new MutableGenotype(g); MutableGenotype mg = new MutableGenotype(g);
mg.clearAttributes(); mg.clearAttributes();
for ( String key : keysToPreserve )
if ( g.hasAttribute(key) )
mg.putAttribute(key, g.getAttribute(key));
mvc.addGenotype(mg); mvc.addGenotype(mg);
} }

3
java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
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@ -241,13 +241,14 @@ 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 VariantContext reduceVCToSamples(VariantContext vc, List<String> samplesToPhase) { private VariantContext reduceVCToSamples(VariantContext vc, List<String> samplesToPhase) {
// for ( String sample : samplesToPhase ) // for ( String sample : samplesToPhase )
// logger.debug(String.format(" Sample %s has genotype %s, het = %s", sample, vc.getGenotype(sample), vc.getGenotype(sample).isHet() )); // logger.debug(String.format(" Sample %s has genotype %s, het = %s", sample, vc.getGenotype(sample), vc.getGenotype(sample).isHet() ));
VariantContext subvc = vc.subContextFromGenotypes(vc.getGenotypes(samplesToPhase).values()); VariantContext subvc = vc.subContextFromGenotypes(vc.getGenotypes(samplesToPhase).values());
// logger.debug("original VC = " + vc); // logger.debug("original VC = " + vc);
// logger.debug("sub VC = " + subvc); // logger.debug("sub VC = " + subvc);
return subvc; return VariantContextUtils.pruneVariantContext(subvc, KEYS_TO_KEEP_IN_REDUCED_VCF );
} }
private List<VariantContext> processQueue(PhasingStats phaseStats, boolean processAll) { private List<VariantContext> processQueue(PhasingStats phaseStats, boolean processAll) {