From f3f1b478085fdd4827d1984d9602f71ec439ba23 Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 20 Mar 2009 16:01:49 +0000 Subject: [PATCH] deal with reverse complemented reads git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@115 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/MismatchHistoWalker.java | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/playground/java/src/org/broadinstitute/sting/gatk/walkers/MismatchHistoWalker.java b/playground/java/src/org/broadinstitute/sting/gatk/walkers/MismatchHistoWalker.java index a2fb8e357..4e0b7cbc0 100755 --- a/playground/java/src/org/broadinstitute/sting/gatk/walkers/MismatchHistoWalker.java +++ b/playground/java/src/org/broadinstitute/sting/gatk/walkers/MismatchHistoWalker.java @@ -54,9 +54,11 @@ public class MismatchHistoWalker extends BasicReadWalker { String refStr = Utils.baseList2string(refSeq).toUpperCase(); String readStr = Utils.baseList2string(readBases).toUpperCase(); + + boolean reverseFlag = read.getReadNegativeStrandFlag(); for ( int i = 0; i < refStr.length(); i++) { if ( refStr.charAt(i) != readStr.charAt(i) ) - mismatchCounts[i]++; + mismatchCounts[(reverseFlag ? (refStr.length()-1-i) : i)]++; } } @@ -70,9 +72,8 @@ public class MismatchHistoWalker extends BasicReadWalker { } public void onTraversalDone() { - for ( int i = 0; i < mismatchCounts.length; i++ ) { - System.out.printf("%3d %10d%n", (i+1), mismatchCounts[i]); - } + for ( int i = 0; i < mismatchCounts.length; i++ ) + System.out.println((i+1) + "\t" + mismatchCounts[i]); } private static Object resizeArray (Object oldArray, int newSize) {