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Quick fix to user error catching

This commit is contained in:
Eric Banks 2012-07-31 15:50:32 -04:00
parent 10111450aa
commit ab53d73459
2 changed files with 3 additions and 3 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
View File

@ -130,12 +130,12 @@ public class CommandLineGATK extends CommandLineExecutable {
// can't close tribble index when writing // can't close tribble index when writing
if ( message.indexOf("Unable to close index for") != -1 ) if ( message.indexOf("Unable to close index for") != -1 )
exitSystemWithUserError(new UserException(t.getCause().getMessage())); exitSystemWithUserError(new UserException(t.getCause() == null ? message : t.getCause().getMessage()));
// disk is full // disk is full
if ( message.indexOf("No space left on device") != -1 ) if ( message.indexOf("No space left on device") != -1 )
exitSystemWithUserError(new UserException(t.getMessage())); exitSystemWithUserError(new UserException(t.getMessage()));
if ( t.getCause().getMessage().indexOf("No space left on device") != -1 ) if ( t.getCause() != null && t.getCause().getMessage().indexOf("No space left on device") != -1 )
exitSystemWithUserError(new UserException(t.getCause().getMessage())); exitSystemWithUserError(new UserException(t.getCause().getMessage()));
} }

2
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -413,7 +413,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test @Test
public void testNsInCigar() { public void testNsInCigar() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "testWithNs.bam", 1, "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + validationDataLocation + "testWithNs.bam -o %s -L 8:141799600-141814700", 1,
Arrays.asList("22c9fd65ce3298bd7fbf400c9c209f29")); Arrays.asList("22c9fd65ce3298bd7fbf400c9c209f29"));
executeTest("test calling on reads with Ns in CIGAR", spec); executeTest("test calling on reads with Ns in CIGAR", spec);
} }