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Done GSA-282: Unindexed traversals crash if a read goes off the end of a contig 

-- Already fixed in the codebase.  Added unindexed bam and integration tests to ensure this is fine going forward.
This commit is contained in:
Mark DePristo 2012-09-04 07:26:01 -04:00
parent d6884e705a
commit 0bd2a872fa
1 changed files with 15 additions and 1 deletions
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16
public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java
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@ -16,13 +16,27 @@ public class PileupWalkerIntegrationTest extends WalkerTest {
executeTest("Testing the standard (no-indel) pileup on three merged FHS pools with 27 deletions in 969 bases", spec);
}
private final static String SingleReadAligningOffChromosome1MD5 = "4a45fe1f85aaa8c4158782f2b6dee2bd";
@Test
public void testSingleReadAligningOffChromosome1() {
String gatk_args = "-T Pileup "
+ " -I " + privateTestDir + "readOffb37contig1.bam"
+ " -R " + b37KGReference
+ " -o %s";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList("4a45fe1f85aaa8c4158782f2b6dee2bd"));
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList(SingleReadAligningOffChromosome1MD5));
executeTest("Testing single read spanning off chromosome 1", spec);
}
@Test
public void testSingleReadAligningOffChromosome1NoIndex() {
String gatk_args = "-T Pileup "
+ " -I " + privateTestDir + "readOffb37contig1.noIndex.bam"
+ " -R " + b37KGReference
+ " -U ALLOW_UNINDEXED_BAM"
+ " -o %s";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList(SingleReadAligningOffChromosome1MD5));
executeTest("Testing single read spanning off chromosome 1 unindexed", spec);
}
}