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Merge branch 'master' of github.com:broadinstitute/gsa-unstable

This commit is contained in:
Mark DePristo 2012-11-28 07:57:05 -05:00
parent 9fd1a3cb9c 79bc878e6a
commit fb1e525e0f
1 changed files with 5 additions and 4 deletions
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9
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
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@ -95,7 +95,8 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) @DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingStats> { public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingStats> {
private static final boolean DEBUG = false; @Argument(fullName="debug", shortName="debug", doc="If specified, print out very verbose debug information (if -l DEBUG is also specified)", required = false)
protected boolean DEBUG = false;
/** /**
* The VCF file we are phasing variants from. * The VCF file we are phasing variants from.
* *
@ -949,7 +950,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
} }
if (DEBUG) logger.debug("\nPhasing table [AFTER CALCULATION]:\n" + sampleHaps + "\n"); if (DEBUG) logger.debug("\nPhasing table [AFTER CALCULATION]:\n" + sampleHaps + "\n");
MaxHaplotypeAndQuality maxHapQual = new MaxHaplotypeAndQuality(sampleHaps, true); MaxHaplotypeAndQuality maxHapQual = new MaxHaplotypeAndQuality(sampleHaps, DEBUG);
double posteriorProb = maxHapQual.maxEntry.getScore().getValue(); double posteriorProb = maxHapQual.maxEntry.getScore().getValue();
if (DEBUG) if (DEBUG)
@ -971,7 +972,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
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 (DEBUG && printDebug) if (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);
@ -981,7 +982,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
private void calculateMaxHapAndPhasingQuality(PhasingTable hapTable, boolean printDebug) { private void calculateMaxHapAndPhasingQuality(PhasingTable hapTable, boolean printDebug) {
hapTable.normalizeScores(); hapTable.normalizeScores();
if (DEBUG && printDebug) if (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: