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Resolving merge conflicts with the new MD5s

This commit is contained in:
Ryan Poplin 2012-08-10 11:47:00 -04:00
parent d7d7ccf789 5f82ffd5d8
commit 2a113977a9
2 changed files with 8 additions and 4 deletions
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4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -276,6 +276,10 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
headerInfo.add(new VCFInfoHeaderLine("extType", 1, VCFHeaderLineType.String, "Extended type of event: SNP, MNP, INDEL, or COMPLEX"));
headerInfo.add(new VCFInfoHeaderLine("QDE", 1, VCFHeaderLineType.Float, "QD value divided by the number of variants found on the haplotype that contained this variant"));
// FILTER fields are added unconditionally as it's not always 100% certain the circumstances
// where the filters are used. For example, in emitting all sites the lowQual field is used
headerInfo.add(new VCFFilterHeaderLine(UnifiedGenotyperEngine.LOW_QUAL_FILTER_NAME, "Low quality"));
vcfWriter.writeHeader(new VCFHeader(headerInfo, samples));
try {

8
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -20,17 +20,17 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "29ebfabcd4a42d4c5c2a576219cffb3d");
HCTest(CEUTRIO_BAM, "", "6b30c7e1b6bbe80d180d9d67441cec12");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "9732313b8a12faa347f6ebe96518c5df");
HCTest(NA12878_BAM, "", "4cdfbfeadef00725974828310558d7d4");
}
@Test
public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "-gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "5e1d49d4110cd96c2e25f8e1da217e9e");
HCTest(CEUTRIO_BAM, "-gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "6183fb6e374976d7087150009685e043");
}
private void HCTestComplexVariants(String bam, String args, String md5) {
@ -41,7 +41,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleComplex() {
HCTestComplexVariants(CEUTRIO_BAM, "", "53df51e6071664725f6e7497f5ee5adf");
HCTestComplexVariants(CEUTRIO_BAM, "", "ab7593a7a60a2e9a66053572f1718df1");
}
}