From 7be01777f6d6c9fffebe92eded4754ea8822a094 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 1 Jul 2013 14:51:15 -0400 Subject: [PATCH] Bugfix for incPos in GenomeLoc -- Shouldn't have taken a GenomeLoc as an argument, as it's a instance method, not a public static --- .../src/org/broadinstitute/sting/utils/GenomeLoc.java | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java index 2a8a271e7..4e8daa0e3 100644 --- a/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java +++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java @@ -560,24 +560,21 @@ public class GenomeLoc implements Comparable, Serializable, HasGenome /** * return a new genome loc, with an incremented position * - * @param loc the old location - * * @return a newly allocated GenomeLoc as loc but with start == loc.getStart() + 1 */ - public GenomeLoc incPos(GenomeLoc loc) { - return incPos(loc, 1); + public GenomeLoc incPos() { + return incPos(1); } /** * return a new genome loc, with an incremented position * - * @param loc the old location * @param by how much to move the start and stop by * * @return a newly allocated GenomeLoc as loc but with start == loc.getStart() + by */ - public GenomeLoc incPos(GenomeLoc loc, int by) { - return new GenomeLoc(loc.getContig(), loc.getContigIndex(), loc.start + by, loc.stop + by); + public GenomeLoc incPos(int by) { + return new GenomeLoc(getContig(), getContigIndex(), start + by, stop + by); } /**