From b07bf1950b639e34295411b1826ec6e758e3f17a Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Sun, 29 Jul 2012 22:19:49 -0400 Subject: [PATCH] Adding an integration test for another feature that I snuck in during a previous commit: we now allow lower-case bases in the REF/ALT alleles of a VCF and upper-case them (this had been turned off because the previous version used Strings to do the uppercasing whereas we stick with byte operations now). --- .../sting/utils/codecs/vcf/VCFIntegrationTest.java | 11 +++++++++++ 1 file changed, 11 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 8f648344d..3948ba971 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 @@ -39,6 +39,17 @@ public class VCFIntegrationTest extends WalkerTest { executeTest("Test reading and writing breakpoint VCF", spec1); } + @Test(enabled = true) + public void testReadingLowerCaseBases() { + String testVCF = privateTestDir + "lowercaseBases.vcf"; + + String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s "; + + String test1 = baseCommand + "-T SelectVariants -V " + testVCF; + WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("e0e308a25e56bde1c664139bb44ed19d")); + executeTest("Test reading VCF with lower-case bases", spec1); + } + @Test(enabled = true) public void testReadingAndWriting1000GSVs() { String testVCF = privateTestDir + "1000G_SVs.chr1.vcf";