From 92fa41045070ef1d938a0d4cc600f500ba1137a9 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 18 Jul 2011 13:43:34 -0400
Subject: [PATCH] Check that it's a valid bam file before parsing or bad things
 can happen

---
 .../gatk/walkers/diffengine/BAMDiffableReader.java     | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
index 15b16ca6b..a1c043365 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
@@ -29,9 +29,7 @@ import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMRecordIterator;
 import net.sf.samtools.util.BlockCompressedInputStream;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
+import java.io.*;
 import java.util.Arrays;
 
 
@@ -102,8 +100,10 @@ public class BAMDiffableReader implements DiffableReader {
         final byte[] BAM_MAGIC = "BAM\1".getBytes();
         final byte[] buffer = new byte[BAM_MAGIC.length];
         try {
-            FileInputStream fstream = new FileInputStream(file);
-            new BlockCompressedInputStream(fstream).read(buffer,0,BAM_MAGIC.length);
+            InputStream fstream = new BufferedInputStream(new FileInputStream(file));
+            if ( !BlockCompressedInputStream.isValidFile(fstream) )
+                return false;
+            new BlockCompressedInputStream(fstream).read(buffer, 0, BAM_MAGIC.length);
             return Arrays.equals(buffer, BAM_MAGIC);
         } catch ( IOException e ) {
             return false;