From 30121534edc706432fc0f7c143f02eb4cd560b9f Mon Sep 17 00:00:00 2001 From: kiran Date: Tue, 14 Apr 2009 13:58:28 +0000 Subject: [PATCH] Outputs the secondary bases and quals (if available) in verbose mode. Prefixed with the tag 'SQ='. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@398 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/PileupWalker.java | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java index 1a6c9b8fd..de9423c0d 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java @@ -44,6 +44,23 @@ public class PileupWalker extends LocusWalker { String extras = ""; if ( VERBOSE ) { + String sqbases = Utils.secondaryBasePileupAsString(reads, offsets); + String sqquals = Utils.secondaryQualPileupAsString(reads, offsets); + + if (sqbases != null && sqquals != null) { + assert(sqbases.length() == sqquals.length()); + + extras += " SQ="; + for (int i = 0; i < sqbases.length(); i++) { + extras += sqbases.charAt(i); + extras += sqquals.charAt(i); + + if (i < sqbases.length() - 1) { + extras += ','; + } + } + } + extras += " BQ=" + Utils.join(",", Utils.qualPileup(reads, offsets)); extras += " MQ=" + Utils.join(",", Utils.mappingQualPileup(reads)); }