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Updating md5s for CountReadsInActiveRegions and HaplotypeCaller to reflect new activity profile mechanics 

-- In this process I discovered a few missed sites in the old code.  The new approach actually produces better HC results than the previous version.
This commit is contained in:
Mark DePristo 2013-01-23 09:47:22 -05:00
parent 8e8126506b
commit 8026199e4c
1 changed files with 11 additions and 11 deletions
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22
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
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "b8f7b741445ce6b6ea491c794ce75c17");
HCTest(CEUTRIO_BAM, "", "c142bc73447c72286ca48f4a4966d9b6");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "a2c63f6e6e51a01019bdbd23125bdb15");
HCTest(NA12878_BAM, "", "d172eb9447015ea50220c6947be145ea");
}
@Test(enabled = false)
@ -84,7 +84,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
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",
"c679ae7f04bdfda896b5c046d35e043c");
"2c56ffc3b7fbbf154ae9ca355780a78f");
}
private void HCTestComplexGGA(String bam, String args, String md5) {
@ -96,13 +96,13 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleGGAComplex() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
"8730a9ebaeecae913dca2fb5a0d4e946");
"66bd513d25b691a5b0c5084924b4a308");
}
@Test
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
"d590c8d6d5e58d685401b65a23846893");
"d0fcbfa2ccce0ca4a2e81f31dc43d79d");
}
private void HCTestComplexVariants(String bam, String args, String md5) {
@ -113,7 +113,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleComplex() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "6c0c441b71848c2eea38ab5e2afe1120");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "7e8a6ed62f866fc47c92af0e255ca180");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -135,7 +135,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "29f1125df5ab27cc937a144ae08ac735");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "602aabbbe710ac90b16e474c869e8a86");
}
// That problem bam came from a user on the forum and it spotted a problem where the ReadClipper
@ -146,14 +146,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
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 WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("31db0a2d9eb07f86e0a89f0d97169072"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("c23b589be3072027ff2da93067dbf549"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
}
@Test
public void HCTestStructuralIndels() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("add0f4f51969b7caeea99005a7ba1aa4"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("a612fe84dd7f80c4ad2d20d27fc6744e"));
executeTest("HCTestStructuralIndels: ", spec);
}
@ -175,7 +175,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
Arrays.asList("8a400b0c46f41447fcc35a907e34f384"));
Arrays.asList("0cb9132967fa9811e04f528be9f686dc"));
executeTest("HC calling on a ReducedRead BAM", spec);
}
@ -183,7 +183,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void testReducedBamWithReadsNotFullySpanningDeletion() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1,
Arrays.asList("4e8121dd9dc90478f237bd6ae4d19920"));
Arrays.asList("36a90309dde1a325c274388e302ffaa5"));
executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec);
}
}