From 3fda8613c384e518de5bfaeaada3a762bf3a8f51 Mon Sep 17 00:00:00 2001 From: kcibul Date: Wed, 15 Apr 2009 15:11:05 +0000 Subject: [PATCH] * minor formatting changes * support for "extended" output git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@428 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/SomaticCoverageWalker.java | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java index f96d78cc0..8c9e0e021 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java @@ -25,9 +25,13 @@ public class SomaticCoverageWalker extends LocusWalker { @Argument(fullName = "normal_sample_name", shortName = "s2", required = true) public String normalSampleName; + @Argument(fullName = "extended", shortName="ext", required=false, defaultValue = "false") + public boolean extendedOutput; + + // --normal_sample_name TCGA-06-0188-10B-01W --tumor_sample_name TCGA-06-0188-01A-01W public void initialize() { - out.println("track type=wiggle_0 name=SomaticCoverage viewLimits=0:1 graphType=heatmap"); + out.println("track type=wiggle_0 name=SomaticCoverage viewLimits=0:1"); } public String walkerType() { return "ByLocus"; } @@ -108,15 +112,18 @@ public class SomaticCoverageWalker extends LocusWalker { if (lastContigIndex != context.getLocation().getContigIndex() || lastPosition + 1 != context.getPosition()) { lastContigIndex = context.getLocation().getContigIndex(); - sb.append("fixedStep\t") - .append("chrom=").append(context.getContig()).append("\t") - .append("start=").append(context.getPosition()).append("\t") + sb.append("fixedStep").append(" ") + .append("chrom=").append(context.getContig()).append(" ") + .append("start=").append(context.getPosition()).append(" ") .append("step=1") .append("\n"); } lastPosition = context.getPosition(); sb.append((isTumorCovered && isNormalCovered)?"1":"0"); + if (extendedOutput) { + sb.append(" ").append(tumorDepth).append(" ").append(normalDepth); + } // sb.append(context.getContig()).append(" "); // sb.append(context.getPosition()).append(" ");