diff --git a/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java index 3757120f8..5f2f35154 100644 --- a/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java +++ b/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java @@ -192,8 +192,8 @@ public class ReadUtils { readFlagNames.put(0x8, "MateUnmapped"); readFlagNames.put(0x10, "Forward"); //readFlagNames.put(0x20, "MateForward"); - readFlagNames.put(0x4, "FirstOfPair"); - readFlagNames.put(0x8, "SecondOfPair"); + readFlagNames.put(0x40, "FirstOfPair"); + readFlagNames.put(0x80, "SecondOfPair"); readFlagNames.put(0x100, "NotPrimary"); readFlagNames.put(0x200, "NON-PF"); readFlagNames.put(0x400, "Duplicate");