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 62bbb0307..18fcdabf2 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java @@ -118,31 +118,40 @@ public class ReadUtils { /** * This enum represents all the different ways in which a read can overlap an interval. * - * NO_OVERLAP: + * NO_OVERLAP_CONTIG: + * read and interval are in different contigs. + * + * NO_OVERLAP_LEFT: + * the read does not overlap the interval. + * + * |----------------| (interval) + * <----------------> (read) + * + * NO_OVERLAP_RIGHT: * the read does not overlap the interval. * * |----------------| (interval) * <----------------> (read) * - * LEFT_OVERLAP: + * OVERLAP_LEFT: * the read starts before the beginning of the interval but ends inside of it * * |----------------| (interval) * <----------------> (read) * - * RIGHT_OVERLAP: + * OVERLAP_RIGHT: * the read starts inside the interval but ends outside of it * * |----------------| (interval) * <----------------> (read) * - * FULL_OVERLAP: + * OVERLAP_LEFT_AND_RIGHT: * the read starts before the interval and ends after the interval * * |-----------| (interval) * <-------------------> (read) * - * CONTAINED: + * OVERLAP_CONTAINED: * the read starts and ends inside the interval * * |----------------| (interval)