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Minor improvements to further reduce debugging output. When running in -samplesToPhase mode, now only including the samples to phase in the output VCF, making it very much smaller. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4881 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-12-20 16:19:47 +00:00
parent ff90c24f28
commit 8604335566
1 changed files with 8 additions and 7 deletions
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15
java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
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@ -176,7 +176,8 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
// todo -- fix samplesToPhase // todo -- fix samplesToPhase
Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), rodNames); Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), rodNames);
writer.writeHeader(new VCFHeader(hInfo, new TreeSet<String>(rodNameToHeader.get(rodNames.get(0)).getGenotypeSamples()))); Set<String> samples = new TreeSet<String>(samplesToPhase == null ? rodNameToHeader.get(rodNames.get(0)).getGenotypeSamples() : samplesToPhase);
writer.writeHeader(new VCFHeader(hInfo, samples));
} }
public boolean generateExtendedEvents() { public boolean generateExtendedEvents() {
@ -241,11 +242,11 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
} }
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 subvc;
} }
@ -899,7 +900,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
public MaxHaplotypeAndQuality(PhasingTable hapTable, boolean printDebug) { public MaxHaplotypeAndQuality(PhasingTable hapTable, boolean printDebug) {
// Marginalize each haplotype to its first 2 positions: // Marginalize each haplotype to its first 2 positions:
hapTable = HaplotypeTableCreator.marginalizeAsNewTable(hapTable); hapTable = HaplotypeTableCreator.marginalizeAsNewTable(hapTable);
if (printDebug) if (DEBUG && printDebug)
logger.debug("\nPhasing table [AFTER MAPPING]:\n" + hapTable + "\n"); logger.debug("\nPhasing table [AFTER MAPPING]:\n" + hapTable + "\n");
calculateMaxHapAndPhasingQuality(hapTable, printDebug); calculateMaxHapAndPhasingQuality(hapTable, printDebug);
@ -909,7 +910,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
private void calculateMaxHapAndPhasingQuality(PhasingTable hapTable, boolean printDebug) { private void calculateMaxHapAndPhasingQuality(PhasingTable hapTable, boolean printDebug) {
hapTable.normalizeScores(); hapTable.normalizeScores();
if (printDebug) if (DEBUG && printDebug)
logger.debug("\nPhasing table [AFTER NORMALIZATION]:\n" + hapTable + "\n"); logger.debug("\nPhasing table [AFTER NORMALIZATION]:\n" + hapTable + "\n");
// Determine the phase at this position: // Determine the phase at this position: