From 88d94d407a20c47cdb1ede0357391265a9c6e822 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 24 Mar 2009 14:34:37 +0000
Subject: [PATCH] Fixed a bug in the parsing of the second end of the pair.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@168 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/playground/illumina/FirecrestFileParser.java         | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/illumina/FirecrestFileParser.java b/java/src/org/broadinstitute/sting/playground/illumina/FirecrestFileParser.java
index 254b8b88d..97a81e99f 100644
--- a/java/src/org/broadinstitute/sting/playground/illumina/FirecrestFileParser.java
+++ b/java/src/org/broadinstitute/sting/playground/illumina/FirecrestFileParser.java
@@ -99,7 +99,8 @@ public class FirecrestFileParser extends AbstractFirecrestFileParser {
             intensities[cycle] = new FourIntensity(fIntensities);
         }
 
-        FourIntensity[] intensities2 = new FourIntensity[(cycle_start > 0 && cycle_stop > 0 && cycle_stop > cycle_start) ? numIntensities : (cycle_stop - cycle_start)];
+        FourIntensity[] intensities2 = new FourIntensity[(cycle_start > 0 && cycle_stop > 0 && cycle_stop > cycle_start) ? (cycle_stop - cycle_start) : numIntensities];
+
         for (int cycle = 0, offset = (cycle_start >= 0 ? cycle_start : 0); cycle < intensities2.length; cycle++) {
             intensities2[cycle] = intensities[offset + cycle];
         }