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Adding hidden printing option. Also, always run UG in mode GENOTYPE_GIVEN_ALLELES given that we don't actually test for the correct alleles (otherwise UG may choose a different allele and we may falsely validate the wrong one).

This commit is contained in:
Eric Banks 2011-09-01 11:40:35 -04:00
parent 0b794b5491
commit 827fe6130c
1 changed files with 33 additions and 7 deletions
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40
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
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@ -253,6 +253,13 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
@Argument(fullName ="sample", shortName ="sn", doc="Name of the sample to validate (in case your VCF/BAM has more than one sample)", required=false) @Argument(fullName ="sample", shortName ="sn", doc="Name of the sample to validate (in case your VCF/BAM has more than one sample)", required=false)
private String sample = ""; private String sample = "";
/**
* Print out discordance sites to standard out.
*/
@Hidden
@Argument(fullName ="print_interesting_sites", shortName ="print_interesting", doc="Print out interesting sites to standard out", required=false)
private boolean printInterestingSites;
private UnifiedGenotyperEngine snpEngine; private UnifiedGenotyperEngine snpEngine;
private UnifiedGenotyperEngine indelEngine; private UnifiedGenotyperEngine indelEngine;
@ -301,7 +308,12 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
UnifiedArgumentCollection uac = new UnifiedArgumentCollection(); UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
uac.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES; uac.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES;
uac.alleles = alleles; uac.alleles = alleles;
if (!bamIsTruth) uac.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
// TODO -- if we change this tool to actually validate against the called allele, then this if statement is needed;
// TODO -- for now, though, we need to be able to validate the right allele (because we only test isVariant below) [EB]
//if (!bamIsTruth)
uac.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
if (mbq >= 0) uac.MIN_BASE_QUALTY_SCORE = mbq; if (mbq >= 0) uac.MIN_BASE_QUALTY_SCORE = mbq;
if (deletions >= 0) if (deletions >= 0)
uac.MAX_DELETION_FRACTION = deletions; uac.MAX_DELETION_FRACTION = deletions;
@ -371,19 +383,26 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
if (call.isVariant()) { if (call.isVariant()) {
if (vcComp.isVariant()) if (vcComp.isVariant())
counter.nAltCalledAlt = 1L; // todo -- may wanna check if the alts called are the same? counter.nAltCalledAlt = 1L; // todo -- may wanna check if the alts called are the same?
else else {
counter.nAltCalledRef = 1L; counter.nAltCalledRef = 1L;
if ( printInterestingSites )
System.out.println("Truth=ALT Call=REF at " + call.getChr() + ":" + call.getStart());
}
} }
// If truth is a confident ALT call // If truth is a confident ALT call
else { else {
if (vcComp.isVariant()) if (vcComp.isVariant()) {
counter.nRefCalledAlt = 1L; counter.nRefCalledAlt = 1L;
else if ( printInterestingSites )
System.out.println("Truth=REF Call=ALT at " + call.getChr() + ":" + call.getStart());
} else
counter.nRefCalledRef = 1L; counter.nRefCalledRef = 1L;
} }
} }
else { else {
counter.nNotConfidentCalls = 1L; counter.nNotConfidentCalls = 1L;
if ( printInterestingSites )
System.out.println("Truth is not confident at " + call.getChr() + ":" + call.getStart());
writeVariant = false; writeVariant = false;
} }
} }
@ -396,17 +415,24 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
if (call.isCalledAlt(callConf)) { if (call.isCalledAlt(callConf)) {
if (vcComp.getAttribute("GV").equals("T")) if (vcComp.getAttribute("GV").equals("T"))
counter.nAltCalledAlt = 1L; counter.nAltCalledAlt = 1L;
else else {
counter.nRefCalledAlt = 1L; counter.nRefCalledAlt = 1L;
if ( printInterestingSites )
System.out.println("Truth=REF Call=ALT at " + call.getChr() + ":" + call.getStart());
}
} }
else if (call.isCalledRef(callConf)) { else if (call.isCalledRef(callConf)) {
if (vcComp.getAttribute("GV").equals("T")) if (vcComp.getAttribute("GV").equals("T")) {
counter.nAltCalledRef = 1L; counter.nAltCalledRef = 1L;
else if ( printInterestingSites )
System.out.println("Truth=ALT Call=REF at " + call.getChr() + ":" + call.getStart());
} else
counter.nRefCalledRef = 1L; counter.nRefCalledRef = 1L;
} }
else { else {
counter.nNotConfidentCalls = 1L; counter.nNotConfidentCalls = 1L;
if ( printInterestingSites )
System.out.println("Truth is not confident at " + call.getChr() + ":" + call.getStart());
writeVariant = false; writeVariant = false;
} }
} }