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

More bad BAM file catching

This commit is contained in:
Eric Banks 2012-07-18 15:26:31 -04:00
parent 659eee13a6
commit b46c85e8b4
1 changed files with 2 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
View File

@ -122,7 +122,8 @@ public class CommandLineGATK extends CommandLineExecutable {
exitSystemWithUserError(new UserException.TooManyOpenFiles());
// malformed BAM looks like a SAM file
if ( message.indexOf("Cannot use index file with textual SAM file") != -1 )
if ( message.indexOf("Cannot use index file with textual SAM file") != -1 ||
message.indexOf("Cannot retrieve file pointers within SAM text files") != -1 )
exitSystemWithSamError(t);
// can't close tribble index when writing