From d0ce56e0183d347a8a6d9f28b649f15b83fb396f Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 9 Apr 2009 20:48:45 +0000
Subject: [PATCH] Remember to take the strand flag into account when
 calculating error rate per cycle as a surrogate for instrument performance.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@347 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/ReadErrorRateWalker.java     | 22 +++++++++----------
 1 file changed, 10 insertions(+), 12 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java
index f854714a6..a3f8857e0 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java
@@ -80,24 +80,22 @@ public class ReadErrorRateWalker extends ReadWalker<boolean[], int[]> {
                     }
 
                     if (nextBestBase != '.') {
-                        errorsPerCycle[cycle] = !(bases[cycle] == compBase || nextBestBase == compBase);
-                        totalMismatches = (!(bases[cycle] == compBase || nextBestBase == compBase)) ? 1 : 0;
+                        if (read.getReadNegativeStrandFlag()) {
+                            errorsPerCycle[bases.length - cycle - 1] = !(bases[cycle] == compBase || nextBestBase == compBase);
+                        } else {
+                            errorsPerCycle[cycle] = !(bases[cycle] == compBase || nextBestBase == compBase);
+                        }
                     }
                 } else {
-                    errorsPerCycle[cycle] = !(bases[cycle] == compBase);
-                    totalMismatches += (!(bases[cycle] == compBase)) ? 1 : 0;
+                    if (read.getReadNegativeStrandFlag()) {
+                        errorsPerCycle[bases.length - cycle - 1] = !(bases[cycle] == compBase);
+                    } else {
+                        errorsPerCycle[cycle] = !(bases[cycle] == compBase);
+                    }
                 }
             }
         }
 
-        /*
-        if (totalMismatches > 4) {
-            for (int cycle = 0; cycle < bases.length; cycle++) { System.out.print((char) bases[cycle]); } System.out.print("\n");
-            for (int cycle = 0, offset = (int) context.getPosition(); cycle < bases.length; cycle++, offset++) { System.out.print((char) contig[offset]); } System.out.print("\n");
-            System.out.println(totalMismatches + "\n");
-        }
-        */
-
         // We encode that we saw a read in the last position of the array.
         // That way we know what to normalize by, and we get thread safety!
         errorsPerCycle[errorsPerCycle.length - 1] = true;