From 7e05b43f407b672bd49e0d686f4a889fff3a7314 Mon Sep 17 00:00:00 2001 From: kcibul Date: Thu, 16 Apr 2009 03:22:49 +0000 Subject: [PATCH] * added some error checking for read groups git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@442 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/SomaticCoverageWalker.java | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java index 8c9e0e021..499843a08 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java @@ -9,6 +9,8 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.cmdLine.Argument; import net.sf.samtools.SAMRecord; +import net.sf.samtools.SAMFileHeader; +import net.sf.samtools.SAMReadGroupRecord; import java.util.List; import java.util.Formatter; @@ -78,7 +80,14 @@ public class SomaticCoverageWalker extends LocusWalker { } String rg = (String) read.getAttribute("RG"); - String sample = read.getHeader().getReadGroup(rg).getSample(); + SAMFileHeader header = read.getHeader(); + SAMReadGroupRecord readGroup = header.getReadGroup(rg); + + if (readGroup == null) { + err.println("WARNING: read " + read.getReadName() + " belongs to read group " + rg + " which isn't in the header!"); + continue; + } + String sample = readGroup.getSample();