From 13be846c2aea5d6388475c037e70a6053efeed69 Mon Sep 17 00:00:00 2001 From: depristo Date: Thu, 4 Jun 2009 18:52:12 +0000 Subject: [PATCH] qualsAsInt argument for Pileup -- fixing stupid bug [again] git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@898 348d0f76-0448-11de-a6fe-93d51630548a --- .../src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java | 2 +- java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java | 1 - 2 files changed, 1 insertion(+), 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 5fa235284..91c976d48 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java @@ -86,7 +86,7 @@ public class PileupWalker extends LocusWalker implements TreeR rodString = "[ROD: " + rodString + "]"; //if ( context.getLocation().getStart() % 1 == 0 ) { - System.out.printf("quals as ints %b%n", qualsAsInts); + //System.out.printf("quals as ints %b%n", qualsAsInts); out.printf("%s%s %s%n", pileup.getPileupString(qualsAsInts), extras, rodString); //} diff --git a/java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java b/java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java index 9e81a4762..a25be3ab0 100755 --- a/java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java +++ b/java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java @@ -84,7 +84,6 @@ public class ReadBackedPileup extends BasicPileup { // In the pileup format, each line represents a genomic position, consisting of chromosome name, // coordinate, reference base, read bases, read qualities and alignment mapping qualities. - System.out.printf("qualsAsInts %b%n", qualsAsInts); //return String.format("%s %s %s %s", getLocation(), getRef(), getBases(), getQuals()); return String.format("%s %s %s %s %s %s", getLocation().getContig(), getLocation().getStart(), // chromosome name and coordinate