diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java index 2de17db14..5d3ef3086 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java @@ -667,7 +667,7 @@ public class ReadUtils { return ReadAndIntervalOverlap.OVERLAP_RIGHT; } - @Ensures({"(result >= read.getUnclippedStart() && result <= read.getUnclippedEnd()) || readIsEntirelyInsertion(read)"}) + @Ensures({"result >= read.getUnclippedStart()", "result <= read.getUnclippedEnd() || readIsEntirelyInsertion(read)"}) public static int getRefCoordSoftUnclippedStart(SAMRecord read) { int start = read.getUnclippedStart(); for (CigarElement cigarElement : read.getCigar().getCigarElements()) { @@ -679,9 +679,13 @@ public class ReadUtils { return start; } - @Ensures({"(result >= read.getUnclippedStart() && result <= read.getUnclippedEnd()) || readIsEntirelyInsertion(read)"}) + @Ensures({"result >= read.getUnclippedStart()", "result <= read.getUnclippedEnd() || readIsEntirelyInsertion(read)"}) public static int getRefCoordSoftUnclippedEnd(SAMRecord read) { int stop = read.getUnclippedStart(); + + if (readIsEntirelyInsertion(read)) + return stop; + int shift = 0; CigarOperator lastOperator = null; for (CigarElement cigarElement : read.getCigar().getCigarElements()) {