zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Check that it's a valid bam file before parsing or bad things can happen

This commit is contained in:
Eric Banks 2011-07-18 13:43:34 -04:00
parent 80b5c5261a
commit 92fa410450
1 changed files with 5 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
View File

@ -29,9 +29,7 @@ import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMRecordIterator; import net.sf.samtools.SAMRecordIterator;
import net.sf.samtools.util.BlockCompressedInputStream; import net.sf.samtools.util.BlockCompressedInputStream;
import java.io.File; import java.io.*;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.Arrays; import java.util.Arrays;
@ -102,8 +100,10 @@ public class BAMDiffableReader implements DiffableReader {
final byte[] BAM_MAGIC = "BAM\1".getBytes(); final byte[] BAM_MAGIC = "BAM\1".getBytes();
final byte[] buffer = new byte[BAM_MAGIC.length]; final byte[] buffer = new byte[BAM_MAGIC.length];
try { try {
FileInputStream fstream = new FileInputStream(file); InputStream fstream = new BufferedInputStream(new FileInputStream(file));
new BlockCompressedInputStream(fstream).read(buffer,0,BAM_MAGIC.length); if ( !BlockCompressedInputStream.isValidFile(fstream) )
return false;
new BlockCompressedInputStream(fstream).read(buffer, 0, BAM_MAGIC.length);
return Arrays.equals(buffer, BAM_MAGIC); return Arrays.equals(buffer, BAM_MAGIC);
} catch ( IOException e ) { } catch ( IOException e ) {
return false; return false;