From c928347c0c05bccf4e99229563bf3714c5915a9f Mon Sep 17 00:00:00 2001 From: asivache Date: Tue, 29 Dec 2009 22:44:18 +0000 Subject: [PATCH] Extended event pileups are more verbose now: following a sequence of 'D','I', and '.' symbols, actual distinct events are listed along with their counts (example: +AAA:3,+AAC:1 for the total of 4 indel observations with 3 reads showing +AAA and one read showing +AAC) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2480 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/PileupWalker.java | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java index a5168c682..b9f664251 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java @@ -33,8 +33,10 @@ import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.Pair; import java.util.ArrayList; +import java.util.List; /** * Prints the alignment in the pileup format. In the pileup format, each line represents a genomic position, @@ -89,7 +91,13 @@ public class PileupWalker extends LocusWalker implements TreeR if ( context.hasExtendedEventPileup() ) { ReadBackedExtendedEventPileup indelPileup = context.getExtendedEventPileup(); - out.printf("%s %s%n", indelPileup.getShortPileupString(), rods); + List> eventCounts = indelPileup.getEventStringsWithCounts(); + out.printf("%s %s ", indelPileup.getShortPileupString(), rods); + int i = 0; + for ( ; i < eventCounts.size() - 1 ; i++ ) { + out.printf("%s:%d,",eventCounts.get(i).first,eventCounts.get(i).second); + } + out.printf("%s:%d%n",eventCounts.get(i).first,eventCounts.get(i).second); } return 1; }