diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java b/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java index 4a253b217..97855080c 100644 --- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java +++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java @@ -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()); diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java index c3684034c..4df899888 100644 --- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java +++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java @@ -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);