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Better error message for reads that begin/end with a deletion in LIBS

This commit is contained in:
Eric Banks 2012-08-16 21:27:07 -04:00
parent 6a2862e8bc
commit 65c594afff
1 changed files with 2 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -159,7 +159,7 @@ public class LocusIteratorByState extends LocusIterator {
return stepForwardOnGenome(); return stepForwardOnGenome();
} else { } else {
if (curElement != null && curElement.getOperator() == CigarOperator.D) if (curElement != null && curElement.getOperator() == CigarOperator.D)
throw new UserException.MalformedBAM(read, "read ends with deletion. Cigar: " + read.getCigarString() + ". This is an indication of a malformed file, but the SAM spec allows reads ending in deletion. If you are sure you want to use this read, re-run your analysis with the extra option: -rf BadCigar"); throw new UserException.MalformedBAM(read, "read ends with deletion. Cigar: " + read.getCigarString() + ". Although the SAM spec technically permits such reads, this is often indicative of malformed files. If you are sure you want to use this file, re-run your analysis with the extra option: -rf BadCigar");
// Reads that contain indels model the genomeOffset as the following base in the reference. Because // Reads that contain indels model the genomeOffset as the following base in the reference. Because
// we fall into this else block only when indels end the read, increment genomeOffset such that the // we fall into this else block only when indels end the read, increment genomeOffset such that the
@ -185,7 +185,7 @@ public class LocusIteratorByState extends LocusIterator {
break; break;
case D: // deletion w.r.t. the reference case D: // deletion w.r.t. the reference
if (readOffset < 0) // we don't want reads starting with deletion, this is a malformed cigar string if (readOffset < 0) // we don't want reads starting with deletion, this is a malformed cigar string
throw new UserException.MalformedBAM(read, "Read starting with deletion. Cigar: " + read.getCigarString() + ". This is an indication of a malformed file, but the SAM spec allows reads starting in deletion. If you are sure you want to use this read, re-run your analysis with the extra option: -rf BadCigar"); throw new UserException.MalformedBAM(read, "read starts with deletion. Cigar: " + read.getCigarString() + ". Although the SAM spec technically permits such reads, this is often indicative of malformed files. If you are sure you want to use this file, re-run your analysis with the extra option: -rf BadCigar");
// should be the same as N case // should be the same as N case
genomeOffset++; genomeOffset++;
done = true; done = true;