From 8d8aed6a67631c341b626c701f303e64e4da2477 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 25 Mar 2011 16:35:43 +0000
Subject: [PATCH] Fix correctness issue when dynamically merging many files.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5512 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/datasources/reads/BAMSchedule.java            | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java b/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java
index 530f7018b..bab22f5aa 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java
@@ -159,6 +159,9 @@ public class BAMSchedule implements CloseableIterator<BAMScheduleEntry> {
             final long readerStopOffset = position();
 
             scheduleIterators.add(new PeekableIterator<BAMScheduleEntry>(new BAMScheduleIterator(reader,readerStartOffset,readerStopOffset,maxChunkCount)));
+
+            // Iterator initialization might move the file pointer.  Make sure it gets reset back to where it was before iterator initialization.
+            position(readerStopOffset);
         }
 
         advance();
@@ -296,6 +299,8 @@ public class BAMSchedule implements CloseableIterator<BAMScheduleEntry> {
     private void write(final ByteBuffer buffer) {
         try {
             scheduleFileChannel.write(buffer);
+            if(buffer.remaining() > 0)
+                throw new ReviewedStingException("Unable to write entire buffer to file.");
         }
         catch(IOException ex) {
             throw new ReviewedStingException("Unable to write data to BAM schedule file.",ex);