From ca0931c01f3a19d7abdd766520ee5b4b6d3f65b4 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 27 Feb 2012 17:05:32 -0500 Subject: [PATCH] Adding test for reading samtools VCF file --- .../sting/utils/codecs/vcf/VCFIntegrationTest.java | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java index ca5fcf419..b7bbae68d 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java @@ -39,4 +39,14 @@ public class VCFIntegrationTest extends WalkerTest { executeTest("Test reading and writing breakpoint VCF", spec1); } + @Test + public void testReadingAndWritingSamtools() { + String testVCF = validationDataLocation + "samtools.vcf"; + + String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s "; + + String test1 = baseCommand + "-T SelectVariants -V " + testVCF; + WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("87d5b180ef5f9dc5aaee4b02601b43a2")); + executeTest("Test reading and writing samtools vcf", spec1); + } }