From 76d833e39b421be832dc2d3014f2d268ea4095d9 Mon Sep 17 00:00:00 2001 From: depristo Date: Wed, 15 Apr 2009 19:12:28 +0000 Subject: [PATCH] Meaningful assert messages git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@435 348d0f76-0448-11de-a6fe-93d51630548a --- java/src/org/broadinstitute/sting/utils/GenomeLoc.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java index bc33f27e3..21afae47e 100644 --- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java +++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java @@ -60,7 +60,7 @@ public class GenomeLoc implements Comparable { } public static int getContigIndex( final String contig ) { - assert contigInfo.getSequenceIndex(contig) != -1; + assert contigInfo.getSequenceIndex(contig) != -1 : "Unknown contig " + contig; return contigInfo.getSequenceIndex(contig); } @@ -125,14 +125,14 @@ public class GenomeLoc implements Comparable { // // -------------------------------------------------------------------------------------------------------------- public GenomeLoc( int contigIndex, final long start, final long stop ) { - assert contigInfo != null; + assert contigInfo != null : "No sequence dictionary defined but index was given"; assert contigIndex >= 0 && contigIndex < contigInfo.size() : "ContigIndex " + contigIndex + " is bad " + contigInfo.size(); - assert start >= 0; - assert stop >= 0; + assert start >= 0 : "Bad start position " + start; + assert stop >= -1 : "Bad stop position " + stop; // a negative -1 indicates it's not a meaningful end position this.contigIndex = contigIndex; this.start = start; - this.stop = stop; + this.stop = stop == -1 ? start : stop; } public GenomeLoc(final SAMRecord read) {