From a8d08ea18d19a827b6e5ae49bb5b89ebdb72b6f0 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 17 Jul 2012 22:18:43 -0400 Subject: [PATCH] As a user pointed out, it is not valid for a GenomeLoc to have a start or stop equal to 0. --- .../org/broadinstitute/sting/utils/GenomeLocParser.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java index b3f4542af..4f2b5b2eb 100644 --- a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java +++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java @@ -304,11 +304,11 @@ public final class GenomeLocParser { return vglHelper(exceptOnError, String.format("The contig index %d is greater than the stored sequence count (%d)", contigIndex, contigInfo.getNSequences())); if ( mustBeOnReference ) { - if (start < 0) - return vglHelper(exceptOnError, String.format("The start position %d is less than 0", start)); + if (start < 1) + return vglHelper(exceptOnError, String.format("The start position %d is less than 1", start)); - if (stop < 0) - return vglHelper(exceptOnError, String.format("The stop position %d is less than 0", stop)); + if (stop < 1) + return vglHelper(exceptOnError, String.format("The stop position %d is less than 1", stop)); int contigSize = contigInfo.getSequence(contigIndex).getSequenceLength(); if (start > contigSize || stop > contigSize)