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Fix bug in GenotypeAndValidate where it doesn't check vc.hasAttribute() before using vc.getAttribute().

This commit is contained in:
Eric Banks 2012-10-24 14:02:50 -04:00
parent 6e421a72d6
commit 5b7b42356b
1 changed files with 20 additions and 17 deletions
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37
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
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@ -245,24 +245,21 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
@Argument(fullName="condition_on_depth", shortName="depth", doc="Condition validation on a minimum depth of coverage by the reads", required=false) @Argument(fullName="condition_on_depth", shortName="depth", doc="Condition validation on a minimum depth of coverage by the reads", required=false)
private int minDepth = -1; private int minDepth = -1;
/** /**
* If your VCF or BAM file has more than one sample and you only want to validate one, use this parameter to choose it.
*/
@Hidden
@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 = "";
/**
* Print out discordance sites to standard out. * Print out discordance sites to standard out.
*/ */
@Hidden @Hidden
@Argument(fullName ="print_interesting_sites", shortName ="print_interesting", doc="Print out interesting sites to standard out", required=false) @Argument(fullName ="print_interesting_sites", shortName ="print_interesting", doc="Print out interesting sites to standard out", required=false)
private boolean printInterestingSites; private boolean printInterestingSites = false;
private UnifiedGenotyperEngine snpEngine; private UnifiedGenotyperEngine snpEngine;
private UnifiedGenotyperEngine indelEngine; private UnifiedGenotyperEngine indelEngine;
private Set<String> samples; private Set<String> samples;
private enum GVstatus {
T, F, NONE
}
public static class CountedData { public static class CountedData {
private long nAltCalledAlt = 0L; private long nAltCalledAlt = 0L;
private long nAltCalledRef = 0L; private long nAltCalledRef = 0L;
@ -368,9 +365,10 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
// Do not operate on variants that are not covered to the optional minimum depth // Do not operate on variants that are not covered to the optional minimum depth
if (!context.hasReads() || (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) { if (!context.hasReads() || (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) {
counter.nUncovered = 1L; counter.nUncovered = 1L;
if (vcComp.getAttribute("GV").equals("T")) final GVstatus status = getGVstatus(vcComp);
if ( status == GVstatus.T )
counter.nAltNotCalled = 1L; counter.nAltNotCalled = 1L;
else if (vcComp.getAttribute("GV").equals("F")) else if ( status == GVstatus.F )
counter.nRefNotCalled = 1L; counter.nRefNotCalled = 1L;
else else
counter.nNoStatusNotCalled = 1L; counter.nNoStatusNotCalled = 1L;
@ -427,10 +425,11 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
// if (!vcComp.hasExtendedAttribute("GV")) // if (!vcComp.hasExtendedAttribute("GV"))
// throw new UserException.BadInput("Variant has no GV annotation in the INFO field. " + vcComp.getChr() + ":" + vcComp.getStart()); // throw new UserException.BadInput("Variant has no GV annotation in the INFO field. " + vcComp.getChr() + ":" + vcComp.getStart());
final GVstatus status = getGVstatus(vcComp);
if (call.isCalledAlt(callConf)) { if (call.isCalledAlt(callConf)) {
if (vcComp.getAttribute("GV").equals("T")) if ( status == GVstatus.T )
counter.nAltCalledAlt = 1L; counter.nAltCalledAlt = 1L;
else if (vcComp.getAttribute("GV").equals("F")) { else if ( status == GVstatus.F ) {
counter.nRefCalledAlt = 1L; counter.nRefCalledAlt = 1L;
if ( printInterestingSites ) if ( printInterestingSites )
System.out.println("Truth=REF Call=ALT at " + call.getChr() + ":" + call.getStart()); System.out.println("Truth=REF Call=ALT at " + call.getChr() + ":" + call.getStart());
@ -439,12 +438,12 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
counter.nNoStatusCalledAlt = 1L; counter.nNoStatusCalledAlt = 1L;
} }
else if (call.isCalledRef(callConf)) { else if (call.isCalledRef(callConf)) {
if (vcComp.getAttribute("GV").equals("T")) { if ( status == GVstatus.T ) {
counter.nAltCalledRef = 1L; counter.nAltCalledRef = 1L;
if ( printInterestingSites ) if ( printInterestingSites )
System.out.println("Truth=ALT Call=REF at " + call.getChr() + ":" + call.getStart()); System.out.println("Truth=ALT Call=REF at " + call.getChr() + ":" + call.getStart());
} }
else if (vcComp.getAttribute("GV").equals("F")) else if ( status == GVstatus.F )
counter.nRefCalledRef = 1L; counter.nRefCalledRef = 1L;
else else
@ -452,9 +451,9 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
} }
else { else {
counter.nNotConfidentCalls = 1L; counter.nNotConfidentCalls = 1L;
if (vcComp.getAttribute("GV").equals("T")) if ( status == GVstatus.T )
counter.nAltNotCalled = 1L; counter.nAltNotCalled = 1L;
else if (vcComp.getAttribute("GV").equals("F")) else if ( status == GVstatus.F )
counter.nRefNotCalled = 1L; counter.nRefNotCalled = 1L;
else else
counter.nNoStatusNotCalled = 1L; counter.nNoStatusNotCalled = 1L;
@ -475,6 +474,10 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
return counter; return counter;
} }
private GVstatus getGVstatus(final VariantContext vc) {
return ( !vc.hasAttribute("GV") ) ? GVstatus.NONE : (vc.getAttribute("GV").equals("T") ? GVstatus.T : GVstatus.F);
}
//--------------------------------------------------------------------------------------------------------------- //---------------------------------------------------------------------------------------------------------------
// //
// reduce // reduce