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Catch samtools exceptions and make them 'BAM Exceptions' asking the user to run Picard's validator and re-index the file before posting anything to the forum. Let's see whether this helps or not. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5658 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-04-18 03:52:43 +00:00
parent e97a5ca161
commit 673772a522
2 changed files with 22 additions and 0 deletions
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19
java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
View File

@ -385,6 +385,25 @@ public abstract class CommandLineProgram {
System.exit(1);
}
public static void exitSystemWithSamError(final Exception e) {
if ( e.getMessage() == null )
throw new ReviewedStingException("SamException found with no message!", e);
errorPrintf("------------------------------------------------------------------------------------------%n");
errorPrintf("A BAM ERROR has occurred (version %s): %n", CommandLineGATK.getVersionNumber());
errorPrintf("The invalid inputs must be corrected before the GATK can proceed%n");
errorPrintf("Please do not post this error to the GATK forum until you have followed the instructions below%n");
errorPrintf("%n");
errorPrintf("Please make sure that your BAM file is well-formed by running Picard's validator on it%n");
errorPrintf("(see http://picard.sourceforge.net/command-line-overview.shtml#ValidateSamFile for details)%n");
errorPrintf("Also, please ensure that your BAM index is not corrupted: delete the current one and regenerate it with 'samtools index'%n");
printDocumentationReference();
errorPrintf("%n");
errorPrintf("MESSAGE: %s%n", e.getMessage().trim());
errorPrintf("------------------------------------------------------------------------------------------%n");
System.exit(1);
}
/**
* used to indicate an error occured

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

@ -92,6 +92,9 @@ public class CommandLineGATK extends CommandLineExecutable {
// We can generate Tribble Exceptions in weird places when e.g. VCF genotype fields are
// lazy loaded, so they aren't caught elsewhere and made into User Exceptions
exitSystemWithUserError(e);
} catch (net.sf.samtools.SAMException e) {
// Let's try this out and see how it is received by our users
exitSystemWithSamError(e);
} catch (Exception e) {
exitSystemWithError(e);
}