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Merge pull request #1467 from broadinstitute/rhl_fix_rprst_is_usable 

Make ReadPosRankSumTest.isUsableRead() account for deletions
This commit is contained in:
Ron Levine 2016-09-08 11:52:54 -04:00 committed by GitHub
parent 3c88e6859f 956b18fbb7
commit e84359a02e
9 changed files with 27 additions and 16 deletions
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2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReadPosRankSumTest.java
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@ -129,7 +129,7 @@ public class ReadPosRankSumTest extends RankSumTest implements StandardAnnotatio
@Override
protected boolean isUsableRead(final GATKSAMRecord read, final int refLoc) {
return super.isUsableRead(read, refLoc) && read.getSoftStart() + read.getCigar().getReadLength() > refLoc;
return super.isUsableRead(read, refLoc) && read.getSoftEnd() >= refLoc;
}

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -423,7 +423,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testStrandAlleleCountsBySample() {
final String MD5 = "564aeeefad92353d66dbb2a2222d5108";
final String MD5 = "994d1d3c53e3878e17d20e1327506d77";
final WalkerTestSpec spec = new WalkerTestSpec(
"-T HaplotypeCaller --disableDithering " +
String.format("-R %s -I %s ", REF, CEUTRIO_BAM) +

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
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@ -88,6 +88,6 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe
//TODO the old MD5 is kept for the record.
//TODO this should be revisit once we get into addressing inaccuracies by the independent allele approach.
// executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "b5ff7530827f4b9039a58bdc8a3560d2");
executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "7421a776c75d0ab5a2ff89d9e7f105ff");
executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "5b76f96b6b74944e0c0d9914700588f0");
}
}

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java
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@ -63,7 +63,7 @@ public class UnifiedGenotyperGeneralPloidySuite2IntegrationTest extends WalkerTe
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","f4092488c9785d800c3f6470af7119ce");
executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","cdaa55c53005deb132f600fa5539c254");
}
@Test(enabled = true)

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
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@ -126,7 +126,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testMismatchedPLs() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
Arrays.asList("1759c156bc45528504398a7ef4ce5bf8"));
Arrays.asList("c41ff9e1e3cfb6bd45d772787dd8e2d3"));
executeTest("test mismatched PLs", spec);
}
}

6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
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@ -72,7 +72,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleComplex1() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "b01df95864808dc67295efc6db37983d");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "79567a4e4307495e880e9782b3a88f7d");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -96,7 +96,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleGGAComplex() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
"828ef27284bd4045148728952b3a7d94");
"558820f3b67f4434a41e0cb96b6469c7");
}
@Test
@ -114,7 +114,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleConsensusModeComplex() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538 -L 20:133041-133161 -L 20:300207-300337",
"060eed2610eed818b2ab55d582eb22ec");
"47894766b0ce7d4aecd89e4938ac1c85");
}
}

12
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
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@ -107,8 +107,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
// this functionality can be adapted to provide input data for whatever you might want in your data
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "3ae2c7e570855f6d6ca58ddd1089a970"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "8bb824886fb0e77d0e8317d69f9d1b62"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "1f19c2b2b528dff502bc1a47701edde7"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "1961007bd98a174a4a1b3e76a9c2f156"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "b34b0b61583628fbd51221627adcdb81"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "63ff771eed3e62340c8938b4963d0add"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "1122a0b3849f42d1c4a654f93b660e1b"});
@ -130,8 +130,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
// this functionality can be adapted to provide input data for whatever you might want in your data
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "8bf132d73cf6b0851ae73c6799f19ba9"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "450906ce3c11860c25b90cf0a56bb1a0"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "49f41972e19f6897659e497d32730dde"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "654c8264cfcbcb71da479761912fbd71"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "4959f20a8bd3327760d94ccc40157f81"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "6ad7855dbf6dda2060aa93a3ee010b3e"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "50e628de2a79cd6887af020b713ca3b8"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "e48bbcf453e63a6ea5eeda05f6865f94"});
@ -148,8 +148,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
// this functionality can be adapted to provide input data for whatever you might want in your data
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "6662cfc41393257dfd6c39f1af1e3843"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "0bc1ca3bff07381a344685b048e76ee4"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "3ff7e3cd9f6b1949d19f52fab53bdb5e"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "dd9fdcae44ab316c04650bf50c38e4b2"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "cb318100ae15cb3dcc342b6142ac6361"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "af0fe243e3b96e59097187cd16ba1597"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "8a094080fb25bbcd39325dcdd62bcf65"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "685025831ac783784d7838e568e35f46"});

13
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -107,7 +107,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeBAMOutFlags() throws IOException {
HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "729ebefdce0d5ea6f535c354c329e6b9", "d38aab5bf8ef0bc7c18e8c909819da84");
HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "a6abb0aa68d3b4d15185a119350e76dc", "d38aab5bf8ef0bc7c18e8c909819da84");
}
@Test
@ -501,5 +501,16 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList(md5));
executeTest("testSetZeroGQsToNoCall", spec);
}
@Test
public void testHaplotypeCallerReadPosRankSum() throws IOException {
final File testBAM = new File(privateTestDir + "testReadPos.snippet.bam");
final String md5Variants = "03b3c464f22a3572f7d66890c18bdda4";
final String md5BAMOut = "2e0843f6e8e90c407825e9c47ce4a32d";
final String base = String.format("-T HaplotypeCaller -R %s -I %s -L 1:3753063 -ip 100 ", REF, testBAM) +
" --no_cmdline_in_header -o %s -bamout %s";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList(md5Variants, md5BAMOut));
executeTest("testHaplotypeCallerReadPosRankSum", spec);
}
}

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
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@ -282,7 +282,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
final WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V " + gVCF.getAbsolutePath(), b37KGReference),
1,
Collections.singletonList("5d8fff160ec6eedb8e02c9207e256073"));
Collections.singletonList("7dfe841940c63415bd5d07ae5d0c69d7"));
spec.disableShadowBCF(); //TODO: Remove when BaseTest.assertAttributesEquals() works with SAC
executeTest("testStrandAlleleCountsBySample", spec);
}