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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).

This commit is contained in:
Eric Banks 2012-07-29 22:19:49 -04:00
parent c4ae9c6cfb
commit b07bf1950b
1 changed files with 11 additions and 0 deletions
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11
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
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@ -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";