diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java index 0c212763d..bd75806dd 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java @@ -62,6 +62,7 @@ public class BQSRIntegrationTest extends WalkerTest { {new BQSRTest(b36KGReference, validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.1RG.bam", "1:10,000,000-10,200,000", "", "43fcba51264cc98bd8466d21e1b96766")}, {new BQSRTest(b36KGReference, validationDataLocation + "originalQuals.1kg.chr1.1-1K.1RG.bam", "1:1-1,000", " -OQ", "48aaf9ac54b97eac3663882a59354ab2")}, {new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-20,000,000", " --solid_recal_mode REMOVE_REF_BIAS", "dac04b9e1e1c52af8d3a50c2e550fda9")}, + {new BQSRTest(b36KGReference, privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam", "1:50,000-80,000", " --solid_nocall_strategy LEAVE_READ_UNRECALIBRATED", "90d70542076715a8605a8d4002614b34")}, {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:anyNameABCD,VCF " + privateTestDir + "vcfexample3.vcf", "600652ee49b9ce1ca2d8ee2d8b7c8211")}, {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:bed " + validationDataLocation + "bqsrKnownTest.bed", "26a04f5a28c40750c603cbe8a926d7bd")}, }; @@ -94,6 +95,20 @@ public class BQSRIntegrationTest extends WalkerTest { executeTest("testBQSRFailWithoutDBSNP", spec); } + @Test + public void testBQSRFailWithSolidNoCall() { + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( + " -T BaseRecalibrator" + + " -R " + b36KGReference + + " -I " + privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam" + + " -L 1:50,000-80,000" + + " --no_plots" + + " -o %s", + 1, // just one output file + UserException.class); + executeTest("testBQSRFailWithSolidNoCall", spec); + } + private static class PRTest { final String args; final String md5;