From 1fb16d54e0b8ce1d4576c7a842bdc59d0dfe4f89 Mon Sep 17 00:00:00 2001 From: kiran Date: Mon, 13 Apr 2009 00:48:21 +0000 Subject: [PATCH] For SAM files that have no alignments and when no reference is specified, contigInfo.getSequence() is null, causing an error when getSequenceName() is called on the resulting null pointer. Check for null instead and return that instead of barfing here. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@374 348d0f76-0448-11de-a6fe-93d51630548a --- java/src/org/broadinstitute/sting/utils/GenomeLoc.java | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java index 54a59123d..e7073b038 100644 --- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java +++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java @@ -325,7 +325,14 @@ public class GenomeLoc implements Comparable { // // Accessors and setters // - public final String getContig() { return contigInfo.getSequence(this.contigIndex).getSequenceName(); } + public final String getContig() { + if (contigInfo != null && contigInfo.getSequence(this.contigIndex) != null) { + return contigInfo.getSequence(this.contigIndex).getSequenceName(); + } + + return null; + } + public final int getContigIndex() { return this.contigIndex; } public final long getStart() { return this.start; } public final long getStop() { return this.stop; }