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Bugfix for Jason F 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1906 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2009-10-24 22:09:27 +00:00
parent 8f381c42fb
commit b4f55df600
1 changed files with 27 additions and 8 deletions
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35
java/src/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalker.java
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@ -71,6 +71,12 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
@Argument(fullName = "clipSequence", shortName = "X", doc = "Remove sequences within reads matching this sequence", required = false) @Argument(fullName = "clipSequence", shortName = "X", doc = "Remove sequences within reads matching this sequence", required = false)
String[] clipSequencesArgs = null; String[] clipSequencesArgs = null;
@Argument(fullName="read", doc="", required=false)
String onlyDoRead = null;
//@Argument(fullName = "keepCompletelyClipped", shortName = "KCC", doc = "Unfortunately, sometimes a read is completely clipped away but with SOFTCLIP_BASES this results in an invalid CIGAR string. ", required = false)
//boolean keepCompletelyClippedReads = false;
// @Argument(fullName = "onlyClipFirstSeqMatch", shortName = "ESC", doc="Only clip the first occurrence of a clipping sequence, rather than all subsequences within a read that match", required = false) // @Argument(fullName = "onlyClipFirstSeqMatch", shortName = "ESC", doc="Only clip the first occurrence of a clipping sequence, rather than all subsequences within a read that match", required = false)
// boolean onlyClipFirstSeqMatch = false; // boolean onlyClipFirstSeqMatch = false;
@ -164,16 +170,19 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
* @return the ReadClipper object describing what should be done to clip this read * @return the ReadClipper object describing what should be done to clip this read
*/ */
public ReadClipper map(char[] ref, SAMRecord read) { public ReadClipper map(char[] ref, SAMRecord read) {
ReadClipper clipper = new ReadClipper(read); if ( onlyDoRead == null || read.getReadName().equals(onlyDoRead) ) {
ReadClipper clipper = new ReadClipper(read);
// //
// run all three clipping modules // run all three clipping modules
// //
clipBadQualityScores(clipper); clipBadQualityScores(clipper);
clipCycles(clipper); clipCycles(clipper);
clipSequences(clipper); clipSequences(clipper);
return clipper;
}
return clipper; return null;
} }
/** /**
@ -311,6 +320,9 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
} }
public ClippingData reduce(ReadClipper clipper, ClippingData data) { public ClippingData reduce(ReadClipper clipper, ClippingData data) {
if ( clipper == null )
return data;
if (data.output != null) { if (data.output != null) {
data.output.addAlignment(clipper.clipRead(clippingRepresentation)); data.output.addAlignment(clipper.clipRead(clippingRepresentation));
} else { } else {
@ -426,6 +438,13 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
if ( ! clippedRead.getReadUnmappedFlag() ) { if ( ! clippedRead.getReadUnmappedFlag() ) {
// we can't process unmapped reads // we can't process unmapped reads
//System.out.printf("%d %d %d%n", stop, start, clippedRead.getReadLength());
if ( (stop + 1 - start) == clippedRead.getReadLength() ) {
// BAM representation issue -- we can't SOFTCLIP away all bases in a read, just leave it alone
logger.info(String.format("Warning, read %s has all bases clip but this can't be represented with SOFTCLIP_BASES, just leaving it alone", clippedRead.getReadName()));
break;
}
if ( start > 0 && stop != clippedRead.getReadLength() - 1 ) if ( start > 0 && stop != clippedRead.getReadLength() - 1 )
throw new RuntimeException(String.format("Cannot apply soft clipping operator to the middle of a read: %s to be clipped at %d-%d", throw new RuntimeException(String.format("Cannot apply soft clipping operator to the middle of a read: %s to be clipped at %d-%d",
clippedRead.getReadName(), start, stop)); clippedRead.getReadName(), start, stop));