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Somehow these md5 updates got lost in my previous git rebase disaster. Sorry for the trouble.

This commit is contained in:
Ryan Poplin 2013-02-04 13:26:18 -05:00
parent 2d518f3063
commit d9fd89ecaa
1 changed files with 6 additions and 6 deletions
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12
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -68,12 +68,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test @Test
public void testHaplotypeCallerMultiSample() { public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "72ce6a5e46644dfd73aeffba9d6131ea"); HCTest(CEUTRIO_BAM, "", "e623c11a2d0e533a4b7fc7e51a7d7d6f");
} }
@Test @Test
public void testHaplotypeCallerSingleSample() { public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "f9d696391f1f337092d70e3abcd32bfb"); HCTest(NA12878_BAM, "", "fe373ccdd2c40c1bed8d7d3cd61cc9c1");
} }
@Test(enabled = false) @Test(enabled = false)
@ -84,7 +84,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test @Test
public void testHaplotypeCallerMultiSampleGGA() { public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
"4e8beb2cdc3d77427f14acf37cea2bd0"); "21a0eae5dbed776ebae471f5e83fca3d");
} }
private void HCTestComplexGGA(String bam, String args, String md5) { private void HCTestComplexGGA(String bam, String args, String md5) {
@ -102,7 +102,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test @Test
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() { public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337", HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
"1d244f2adbc72a0062eb673d56cbb5a8"); "efc571f7b64bc13849b0776c4951dadb");
} }
private void HCTestComplexVariants(String bam, String args, String md5) { private void HCTestComplexVariants(String bam, String args, String md5) {
@ -113,7 +113,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test @Test
public void testHaplotypeCallerMultiSampleComplex() { public void testHaplotypeCallerMultiSampleComplex() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "a1bc844f62a9cb60dbb70d00ad36b85d"); HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "3312875416a1a4274a864977effd0afa");
} }
private void HCTestSymbolicVariants(String bam, String args, String md5) { private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -146,7 +146,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test @Test
public void HCTestProblematicReadsModifiedInActiveRegions() { public void HCTestProblematicReadsModifiedInActiveRegions() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965"; final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("103c91c4a78164949e166d3d27eb459b")); final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("5ac992d47aa6b7c220e5bb7c07444de1"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec); executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
} }