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 499843a08..72a8343cc 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java @@ -62,6 +62,7 @@ public class SomaticCoverageWalker extends LocusWalker { List reads = context.getReads(); int tumorDepth = 0; int normalDepth = 0; + StringBuilder readNames = new StringBuilder(); for ( int i = 0; i < reads.size(); i++ ) { SAMRecord read = reads.get(i); @@ -98,6 +99,7 @@ public class SomaticCoverageWalker extends LocusWalker { } else { throw new RuntimeException("Unknown Sample Name: " + sample); } + readNames.append(read.getReadName()).append("+").append(read.getAlignmentStart()).append("+").append(read.getCigarString()); } @@ -129,9 +131,12 @@ public class SomaticCoverageWalker extends LocusWalker { } lastPosition = context.getPosition(); + if (extendedOutput) { + sb.append(context.getPosition()).append(" "); + } sb.append((isTumorCovered && isNormalCovered)?"1":"0"); if (extendedOutput) { - sb.append(" ").append(tumorDepth).append(" ").append(normalDepth); + sb.append(" ").append(tumorDepth).append(" ").append(normalDepth).append(" ").append(readNames); } // sb.append(context.getContig()).append(" ");