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Fixing but for reads with cigars like 9S54H 

When hard-clipping predict when the read is going to be fully hard clipped to the point where only soft/hard-clips are left in the read and preemptively eliminate the read before the SAMRecord mathematics on malformed cigars kills the GATK.
This commit is contained in:
Mauricio Carneiro 2012-07-02 12:28:28 -04:00
parent 9ee58d323a
commit 88a02fa2cb
2 changed files with 5 additions and 2 deletions
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5
public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java
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@ -285,7 +285,10 @@ public class ClippingOp {
@Requires({"start <= stop", "start == 0 || stop == read.getReadLength() - 1"})
private GATKSAMRecord hardClip(GATKSAMRecord read, int start, int stop) {
if (start == 0 && stop == read.getReadLength() - 1)
final int firstBaseAfterSoftClips = read.getAlignmentStart() - read.getSoftStart();
final int lastBaseBeforeSoftClips = read.getSoftEnd() - read.getSoftStart();
if (start == firstBaseAfterSoftClips && stop == lastBaseBeforeSoftClips) // note that if the read has no soft clips, these constants will be 0 and read length - 1 (beauty of math).
return GATKSAMRecord.emptyRead(read);

2
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
View File

@ -520,7 +520,7 @@ public class ReadUtils {
if (allowGoalNotReached) {
return new Pair<Integer, Boolean>(CLIPPING_GOAL_NOT_REACHED, false);
} else {
throw new ReviewedStingException("Somehow the requested coordinate is not covered by the read. Too many deletions?");
throw new ReviewedStingException("Somehow the requested coordinate is not covered by the read. Alignment " + alignmentStart + " | " + cigar);
}
}