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

Handle RuntimeExceptions thrown by Picard that are really User Errors. I will add unit tests for these as best I can later.

This commit is contained in:
Eric Banks 2012-07-18 13:56:35 -04:00
parent ae08d35138
commit 4c730542f0
2 changed files with 17 additions and 9 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
View File

@ -369,9 +369,9 @@ public abstract class CommandLineProgram {
System.exit(1); System.exit(1);
} }
public static void exitSystemWithSamError(final Exception e) { public static void exitSystemWithSamError(final Throwable t) {
if ( e.getMessage() == null ) if ( t.getMessage() == null )
throw new ReviewedStingException("SamException found with no message!", e); throw new ReviewedStingException("SamException found with no message!", t);
errorPrintf("------------------------------------------------------------------------------------------%n"); errorPrintf("------------------------------------------------------------------------------------------%n");
errorPrintf("A BAM ERROR has occurred (version %s): %n", CommandLineGATK.getVersionNumber()); errorPrintf("A BAM ERROR has occurred (version %s): %n", CommandLineGATK.getVersionNumber());
@ -383,7 +383,7 @@ public abstract class CommandLineProgram {
errorPrintf("Also, please ensure that your BAM index is not corrupted: delete the current one and regenerate it with 'samtools index'%n"); errorPrintf("Also, please ensure that your BAM index is not corrupted: delete the current one and regenerate it with 'samtools index'%n");
printDocumentationReference(); printDocumentationReference();
errorPrintf("%n"); errorPrintf("%n");
errorPrintf("MESSAGE: %s%n", e.getMessage().trim()); errorPrintf("MESSAGE: %s%n", t.getMessage().trim());
errorPrintf("------------------------------------------------------------------------------------------%n"); errorPrintf("------------------------------------------------------------------------------------------%n");
System.exit(1); System.exit(1);
} }

18
public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
View File

@ -101,20 +101,28 @@ public class CommandLineGATK extends CommandLineExecutable {
// TODO: Should Picard exceptions be, in general, UserExceptions or ReviewedStingExceptions? // TODO: Should Picard exceptions be, in general, UserExceptions or ReviewedStingExceptions?
exitSystemWithError(e); exitSystemWithError(e);
} catch (SAMException e) { } catch (SAMException e) {
checkForTooManyOpenFilesProblem(e.getMessage()); checkForMaskedUserErrors(e);
exitSystemWithSamError(e); exitSystemWithSamError(e);
} catch (OutOfMemoryError e) { } catch (OutOfMemoryError e) {
exitSystemWithUserError(new UserException.NotEnoughMemory()); exitSystemWithUserError(new UserException.NotEnoughMemory());
} catch (Throwable t) { } catch (Throwable t) {
checkForTooManyOpenFilesProblem(t.getMessage()); checkForMaskedUserErrors(t);
exitSystemWithError(t); exitSystemWithError(t);
} }
} }
private static void checkForTooManyOpenFilesProblem(String message) { private static void checkForMaskedUserErrors(final Throwable t) {
// Special case the "Too many open files" error because it's a common User Error for which we know what to do final String message = t.getMessage();
if ( message != null && message.indexOf("Too many open files") != -1 ) if ( message == null )
return;
// we know what to do about the common "Too many open files" error
if ( message.indexOf("Too many open files") != -1 )
exitSystemWithUserError(new UserException.TooManyOpenFiles()); exitSystemWithUserError(new UserException.TooManyOpenFiles());
// Malformed BAM looks like a SAM file
if ( message.indexOf("Cannot use index file with textual SAM file") != -1 )
exitSystemWithSamError(t);
} }
/** /**