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Changing HardClipper contract to allow UNMAPPED reads 

shifted the contract to functions that operate on reference based coordinates. The clipper should do the right thing with unmapped reads, but it needs more testing (Ryan is using it at the moment and says it works). Will write some unit tests.
This commit is contained in:
Mauricio Carneiro 2011-12-15 11:08:19 -05:00
parent 598a21d01c
commit 62a2e335bc
2 changed files with 2 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java
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@ -247,7 +247,7 @@ public class ClippingOp {
return newCigar;
}
@Requires({"start <= stop", "start == 0 || stop == read.getReadLength() - 1", "!read.getReadUnmappedFlag()"})
@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)
return new GATKSAMRecord(read.getHeader());

1
public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
View File

@ -58,6 +58,7 @@ public class ReadClipper {
return hardClipByReferenceCoordinates(refStart, -1);
}
@Requires("!read.getReadUnmappedFlag()")
protected GATKSAMRecord hardClipByReferenceCoordinates(int refStart, int refStop) {
int start = (refStart < 0) ? 0 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart, ReadUtils.ClippingTail.RIGHT_TAIL);
int stop = (refStop < 0) ? read.getReadLength() - 1 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop, ReadUtils.ClippingTail.LEFT_TAIL);