diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java index 667b325ed..e16ef3125 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java @@ -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); + } }