From 761d70faa11bb2ac5a7b70b746df99ee8dc4d548 Mon Sep 17 00:00:00 2001 From: depristo Date: Tue, 21 Jul 2009 21:58:27 +0000 Subject: [PATCH] Better printing of multiple rods -- now produces a comma-separated set of values git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1289 348d0f76-0448-11de-a6fe-93d51630548a --- .../broadinstitute/sting/gatk/walkers/PileupWalker.java | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java index d218c8ff6..56cfc0948 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java @@ -32,6 +32,8 @@ import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.ReadBackedPileup; import org.broadinstitute.sting.utils.Utils; +import java.util.ArrayList; + /** * samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list] [-iscg] [-T theta] [-N nHap] [-r pairDiffRate] * @@ -125,12 +127,13 @@ public class PileupWalker extends LocusWalker implements TreeR * @return String representation of the reference-ordered data. */ private String getReferenceOrderedData( RefMetaDataTracker tracker ) { - String rodString = ""; + ArrayList rodStrings = new ArrayList(); for ( ReferenceOrderedDatum datum : tracker.getAllRods() ) { if ( datum != null && ! (datum instanceof rodDbSNP)) { - rodString += datum.toSimpleString(); + rodStrings.add(datum.toSimpleString()); } } + String rodString = Utils.join(", ", rodStrings); rodDbSNP dbsnp = (rodDbSNP)tracker.lookup("dbSNP", null); if ( dbsnp != null )