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Test for missing read group 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4192 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-09-02 14:22:13 +00:00
parent acd6bd2430
commit 590bb50d16
1 changed files with 13 additions and 1 deletions
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14
java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
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@ -86,7 +86,7 @@ public class CoverageUtils {
Map<SAMReadGroupRecord, int[]> countsByRG = new HashMap<SAMReadGroupRecord,int[]>(); Map<SAMReadGroupRecord, int[]> countsByRG = new HashMap<SAMReadGroupRecord,int[]>();
for ( PileupElement e : context.getBasePileup() ) { for ( PileupElement e : context.getBasePileup() ) {
if ( e.getMappingQual() >= minMapQ && e.getMappingQual() <= maxMapQ && ( e.getQual() >= minBaseQ && e.getQual() <= maxBaseQ || e.isDeletion() ) ) { if ( e.getMappingQual() >= minMapQ && e.getMappingQual() <= maxMapQ && ( e.getQual() >= minBaseQ && e.getQual() <= maxBaseQ || e.isDeletion() ) ) {
SAMReadGroupRecord readGroup = e.getRead().getReadGroup(); SAMReadGroupRecord readGroup = getReadGroup(e.getRead());
if ( ! countsByRG.keySet().contains(readGroup) ) { if ( ! countsByRG.keySet().contains(readGroup) ) {
countsByRG.put(readGroup,new int[6]); countsByRG.put(readGroup,new int[6]);
updateCounts(countsByRG.get(readGroup),e); updateCounts(countsByRG.get(readGroup),e);
@ -112,4 +112,16 @@ public class CoverageUtils {
} }
} }
} }
private static SAMReadGroupRecord getReadGroup(SAMRecord r) {
SAMReadGroupRecord rg = r.getReadGroup();
if ( rg == null ) {
String msg = "Read "+r.getReadName()+" lacks read group information.";
msg += " Please associate all reads with read groups [recommended]\n";
msg += " Or run with -rf MissingReadGroup [not recommended]";
throw new StingException(msg);
}
return rg;
}
} }