From 34e566c90d61cecdd1c43baf3b0ccc45c5304e71 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 11 Feb 2010 17:00:04 +0000
Subject: [PATCH] Fixed bug where new sharding system wasn't grabbing the reads
 that start at the end of a bin.  Caused by what I currently believe to be a
 bug in Picard -- will verify with Alec.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2826 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/net/sf/samtools/BAMFileReader2.java | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/java/src/net/sf/samtools/BAMFileReader2.java b/java/src/net/sf/samtools/BAMFileReader2.java
index e2c4b8aed..6d954fc11 100644
--- a/java/src/net/sf/samtools/BAMFileReader2.java
+++ b/java/src/net/sf/samtools/BAMFileReader2.java
@@ -399,8 +399,6 @@ class BAMFileReader2
 
         public SAMRecord next() {
             final SAMRecord result = mNextRecord;
-            if(result.getAlignmentStart() <= 11632602 && result.getAlignmentEnd() >= 11632602)
-                System.out.printf("11632602: %s%n", result.getReadName());            
             advance();
             return result;
         }
@@ -495,7 +493,7 @@ class BAMFileReader2
             throws IOException {
             while (true) {
                 // Advance to next file block if necessary
-                while (mCompressedInputStream.getFilePointer() >= mFilePointerLimit) {
+                while (mCompressedInputStream.getFilePointer() > mFilePointerLimit) {
                     if (mFilePointers == null ||
                         mFilePointerIndex >= mFilePointers.length) {
                         return null;