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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
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public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
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@ -122,7 +122,8 @@ public class CommandLineGATK extends CommandLineExecutable {
exitSystemWithUserError(new UserException.TooManyOpenFiles()); exitSystemWithUserError(new UserException.TooManyOpenFiles());
// malformed BAM looks like a SAM file // 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); exitSystemWithSamError(t);
// can't close tribble index when writing // can't close tribble index when writing