From 28c1330b4b1f3cbc5f6858624f4c6b12c1858a2e Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 24 Mar 2009 21:59:25 +0000
Subject: [PATCH] Fixed a bug wherein the loop variable for the second end of
 the pair was actually looping over the entire raw read (first and second ends
 combined).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@178 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/fourbasecaller/FourBaseRecaller.java  | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/fourbasecaller/FourBaseRecaller.java b/java/src/org/broadinstitute/sting/playground/fourbasecaller/FourBaseRecaller.java
index b554da162..897eb5728 100644
--- a/java/src/org/broadinstitute/sting/playground/fourbasecaller/FourBaseRecaller.java
+++ b/java/src/org/broadinstitute/sting/playground/fourbasecaller/FourBaseRecaller.java
@@ -51,7 +51,7 @@ public class FourBaseRecaller {
             FourIntensity[] intensities = ffp1.next().getIntensities();
             String rsq = (CYCLE_START == 0) ? bfp1.next().getFirstReadSequence() : bfp1.next().getSecondReadSequence();
 
-            for (int cycle = 0; cycle < intensities.length; cycle++) {
+            for (int cycle = 0; cycle < readLength; cycle++) {
                 FourIntensity sig = intensities[cycle];
 
                 if      (rsq.charAt(cycle) == 'A') { cmeans[cycle].add(Nucleotide.A, sig); }
@@ -73,7 +73,7 @@ public class FourBaseRecaller {
             FourIntensity[] intensities = ffp2.next().getIntensities();
             String rsq = (CYCLE_START == 0) ? bfp2.next().getFirstReadSequence() : bfp2.next().getSecondReadSequence();
 
-            for (int cycle = 0; cycle < intensities.length; cycle++) {
+            for (int cycle = 0; cycle < readLength; cycle++) {
                 FourIntensity sig = intensities[cycle];
                 NucleotideChannelMeans mus = cmeans[cycle];
 
@@ -103,11 +103,11 @@ public class FourBaseRecaller {
 
             FourIntensity[] intensities = ffp3.next().getIntensities();
 
-            byte[] asciiseq = new byte[intensities.length];
-            byte[] bestqual = new byte[intensities.length];
-            byte[] nextbestqual = new byte[intensities.length];
+            byte[] asciiseq = new byte[readLength];
+            byte[] bestqual = new byte[readLength];
+            byte[] nextbestqual = new byte[readLength];
 
-            for (int cycle = 0; cycle < intensities.length; cycle++) {
+            for (int cycle = 0; cycle < readLength; cycle++) {
                 FourIntensity fi = intensities[cycle];
 
                 double[] likes = new double[4];