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add output for number of variants that validated as true 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2942 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-03-05 18:57:44 +00:00
parent 037ac9c9af
commit 7fa0f77721
1 changed files with 13 additions and 5 deletions
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18
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCF.java
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@ -50,6 +50,7 @@ public class PlinkToVCF extends RodWalker<VCFRecord,Integer> {
private int numHWViolations = 0;
private int numNoCallViolations = 0;
private int numHomVarViolations = 0;
private int numTrueVariants = 0;
private HashMap<String,String> samplesToPopulation;
@ -121,12 +122,13 @@ public class PlinkToVCF extends RodWalker<VCFRecord,Integer> {
public void onTraversalDone(Integer finalReduce) {
if ( vcfWriter != null )
vcfWriter.close();
System.out.println(String.format("Total number of records processed:\t\t%d", numRecords));
System.out.println(String.format("Number of Hardy-Weinberg violations:\t\t%d (%d%%)", numHWViolations, 100*numHWViolations/numRecords));
System.out.println(String.format("Number of no-call violations:\t\t\t%d (%d%%)", numNoCallViolations, 100*numNoCallViolations/numRecords));
System.out.println(String.format("Number of homozygous variant violations:\t%d (%d%%)", numHomVarViolations, 100*numHomVarViolations/numRecords));
System.out.println(String.format("Total number of records processed:\t\t\t%d", numRecords));
System.out.println(String.format("Number of Hardy-Weinberg violations:\t\t\t%d (%d%%)", numHWViolations, 100*numHWViolations/numRecords));
System.out.println(String.format("Number of no-call violations:\t\t\t\t%d (%d%%)", numNoCallViolations, 100*numNoCallViolations/numRecords));
System.out.println(String.format("Number of homozygous variant violations:\t\t%d (%d%%)", numHomVarViolations, 100*numHomVarViolations/numRecords));
int goodRecords = numRecords - numHWViolations - numNoCallViolations - numHomVarViolations;
System.out.println(String.format("Number of records passing all filters:\t\t%d (%d%%)", goodRecords, 100*goodRecords/numRecords));
System.out.println(String.format("Number of records passing all filters:\t\t\t%d (%d%%)", goodRecords, 100*goodRecords/numRecords));
System.out.println(String.format("Number of passing records that validated as true:\t%d (%d%%)", numTrueVariants, 100*numTrueVariants/goodRecords));
}
@ -158,15 +160,19 @@ public class PlinkToVCF extends RodWalker<VCFRecord,Integer> {
double hetProp = (double)vContext.getHetCount() / (double)vContext.getNSamples();
double homVarProp = (double)vContext.getHomVarCount() / (double)vContext.getNSamples();
boolean isViolation = false;
if ( noCallProp > maxNoCall ) {
record.setFilterString("HighNoCallRate");
numNoCallViolations++;
isViolation = true;
} else if ( hwScore > maxHardy ) {
record.setFilterString("HardyWeinbergViolation");
numHWViolations++;
isViolation = true;
} else if ( homVarProp > maxHomNonref) {
record.setFilterString("TooManyHomVars");
numHomVarViolations++;
isViolation = true;
}
numRecords++;
@ -179,6 +185,8 @@ public class PlinkToVCF extends RodWalker<VCFRecord,Integer> {
infoMap.put("HW", String.format("%.2f", hwScore));
Set<Allele> altAlleles = vContext.getAlternateAlleles();
int altAlleleCount = altAlleles.size() == 0 ? 0 : vContext.getChromosomeCount(altAlleles.iterator().next());
if ( !isViolation && altAlleleCount > 0 )
numTrueVariants++;
infoMap.put(VCFRecord.ALLELE_COUNT_KEY, String.format("%d", altAlleleCount));
infoMap.put(VCFRecord.ALLELE_NUMBER_KEY, String.format("%d", vContext.getChromosomeCount()));
record.addInfoFields(infoMap);