zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Error checking for bad input (thanks, Aaron). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3120 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-04-04 03:17:01 +00:00
parent 27fb6f7594
commit 56eb15f91f
1 changed files with 17 additions and 12 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
View File

@ -103,6 +103,9 @@ public class SequenomValidationConverter extends RodWalker<VCFRecord,Integer> {
} }
public void onTraversalDone(Integer finalReduce) { public void onTraversalDone(Integer finalReduce) {
if ( sampleNames == null )
sampleNames = new TreeSet<String>();
VCFWriter vcfWriter = new VCFWriter(vcfFile); VCFWriter vcfWriter = new VCFWriter(vcfFile);
// set up the info and filter headers // set up the info and filter headers
@ -125,6 +128,7 @@ public class SequenomValidationConverter extends RodWalker<VCFRecord,Integer> {
hInfo.add(new VCFHeaderLine("ValidationMetrics_SamplesAssayed", String.format("%d", sampleNames.size()))); hInfo.add(new VCFHeaderLine("ValidationMetrics_SamplesAssayed", String.format("%d", sampleNames.size())));
System.out.println(String.format("Total number of records processed:\t\t\t%d", numRecords)); System.out.println(String.format("Total number of records processed:\t\t\t%d", numRecords));
hInfo.add(new VCFHeaderLine("ValidationMetrics_RecordsProcessed", String.format("%d", numRecords))); hInfo.add(new VCFHeaderLine("ValidationMetrics_RecordsProcessed", String.format("%d", numRecords)));
if ( numRecords > 0 ) {
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 Hardy-Weinberg violations:\t\t\t%d (%d%%)", numHWViolations, 100*numHWViolations/numRecords));
hInfo.add(new VCFHeaderLine("ValidationMetrics_HardyWeinbergViolations", String.format("\"%d (%d%%)\"", numHWViolations, 100*numHWViolations/numRecords))); hInfo.add(new VCFHeaderLine("ValidationMetrics_HardyWeinbergViolations", String.format("\"%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 no-call violations:\t\t\t\t%d (%d%%)", numNoCallViolations, 100*numNoCallViolations/numRecords));
@ -136,6 +140,7 @@ public class SequenomValidationConverter extends RodWalker<VCFRecord,Integer> {
hInfo.add(new VCFHeaderLine("ValidationMetrics_RecordsPassingFilters", String.format("\"%d (%d%%)\"", goodRecords, 100*goodRecords/numRecords))); hInfo.add(new VCFHeaderLine("ValidationMetrics_RecordsPassingFilters", String.format("\"%d (%d%%)\"", goodRecords, 100*goodRecords/numRecords)));
System.out.println(String.format("Number of passing records that are polymorphic:\t\t%d (%d%%)", numTrueVariants, 100*numTrueVariants/goodRecords)); System.out.println(String.format("Number of passing records that are polymorphic:\t\t%d (%d%%)", numTrueVariants, 100*numTrueVariants/goodRecords));
hInfo.add(new VCFHeaderLine("ValidationMetrics_PolymorphicPassingRecords", String.format("\"%d (%d%%)\"", numTrueVariants, 100*numTrueVariants/goodRecords))); hInfo.add(new VCFHeaderLine("ValidationMetrics_PolymorphicPassingRecords", String.format("\"%d (%d%%)\"", numTrueVariants, 100*numTrueVariants/goodRecords)));
}
VCFHeader header = new VCFHeader(hInfo, sampleNames); VCFHeader header = new VCFHeader(hInfo, sampleNames);
vcfWriter.writeHeader(header); vcfWriter.writeHeader(header);