From f9ce9962c4cb55e15db17ef52944bb9b9ff409c1 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 3 Apr 2012 10:53:48 -0400 Subject: [PATCH] Minor changes to verbose mode --- .../sting/gatk/walkers/PileupWalker.java | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java index 8dfa26390..ac84bbddc 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java @@ -116,21 +116,28 @@ public class PileupWalker extends LocusWalker implements TreeR return rodString; } - + + private static final String verboseDelimiter = "@"; // it's ugly to use "@" but it's literally the only usable character not allowed in read names + private static String createVerboseOutput(final ReadBackedPileup pileup) { final StringBuilder sb = new StringBuilder(); boolean isFirst = true; + sb.append(pileup.getNumberOfDeletions()); + sb.append(" "); + for ( PileupElement p : pileup ) { if ( isFirst ) isFirst = false; else sb.append(","); sb.append(p.getRead().getReadName()); - sb.append(":"); + sb.append(verboseDelimiter); sb.append(p.getOffset()); - sb.append(":"); + sb.append(verboseDelimiter); sb.append(p.getRead().getReadLength()); + sb.append(verboseDelimiter); + sb.append(p.getRead().getMappingQuality()); } return sb.toString(); }