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Merge pull request #883 from broadinstitute/rhl_hc_mq0 

Exclude MappingQualityZero from default annotations
This commit is contained in:
Geraldine Van der Auwera 2015-03-23 12:59:08 -04:00
parent 244dbe8634 46668d469a
commit 0a45b2d79d
5 changed files with 89 additions and 86 deletions
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4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java
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@ -104,7 +104,7 @@ public class MappingQualityZero extends InfoFieldAnnotation implements StandardA
private Map<String, Object> annotatePileup(final ReferenceContext ref,
final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
if ( stratifiedContexts.isEmpty() )
return null;
int mq0 = 0;
@ -123,7 +123,7 @@ public class MappingQualityZero extends InfoFieldAnnotation implements StandardA
private Map<String, Object> annotateWithLikelihoods(final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap,
final VariantContext vc) {
if (stratifiedPerReadAlleleLikelihoodMap == null)
if ( stratifiedPerReadAlleleLikelihoodMap == null )
return null;
int mq0 = 0;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
View File

@ -356,7 +356,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
*/
@Advanced
@Argument(fullName="excludeAnnotation", shortName="XA", doc="One or more specific annotations to exclude", required=false)
protected List<String> annotationsToExclude = new ArrayList<>(Arrays.asList(new String[]{"SpanningDeletions", "TandemRepeatAnnotator"}));
protected List<String> annotationsToExclude = new ArrayList<>(Arrays.asList(new String[]{"SpanningDeletions", "TandemRepeatAnnotator", "MappingQualityZero"}));
/**
* Which groups of annotations to add to the output VCF file. The single value 'none' removes the default group. See

10
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
View File

@ -72,7 +72,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleComplex1() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "dc7906ed73dc071162c98e4bbe77df44");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "329e57675a6bab117597f02e3f109095");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -84,7 +84,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
// TODO -- need a better symbolic allele test
@Test
public void testHaplotypeCallerSingleSampleSymbolic() {
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "845e795a345400a37c0dafdd5ce2f9ac");
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "2bddd2bf5427142bf2235daa8589efee");
}
private void HCTestComplexGGA(String bam, String args, String md5) {
@ -96,13 +96,13 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleGGAComplex() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
"d27dba3772a68f254d00b247f09099ec");
"4c12c04c34c782b25df78d37868e742d");
}
@Test
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
"0eb6ce85c70b152062a5af63b6da3e8f");
"c3fc8876b9b7247f68d758b8a9d60fe5");
}
private void HCTestComplexConsensusMode(String bam, String args, String md5) {
@ -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",
"523d3fb07b40d8c2637e82ba7a6e2a5b");
"b6576ef09027cb22fa02efda67f7139d");
}
}

60
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
View File

@ -74,12 +74,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
// 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, "646ec07bd026da1e72b5e789f5aa3a3d"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "cb598bee733db0461f6a24d265daed45"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "c53ecb02a41511123dc4e1573dd516f6"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "9dbe7721ebfba9aefcfbfd1bdd62f2c4"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "4c99694b14beffd694f9738697b8f9d5"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "87d1e673e2512aefdceddd0293e4f346"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "6bfe8418aefa0d5d04bdc8f5f31bbb97"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "8daf142d0f42967b9c59aae4580a18c5"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "1ad6d0d5764e2bc0839af4b79f1bd351"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "00aa548e22334fc121f0c8bee2b05d7a"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "2e64530bfc8cb0a3ad72cc5d11d4694b"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "c236b1f6bfbbbc258d3077d75bb9e552"});
return tests.toArray(new Object[][]{});
}
@ -93,13 +93,13 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
// 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, "83b96e3e364821c51e6a2c2a64616b24"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "f38178834961798d79e7190dbca004bf"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "a6db14e73e0a270b9d3e2035acfc1d2f"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "afede7dbbcbe0e1af4abba7fc7bef479"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "853bd2f47496b3e8d1fe85657e4bf812"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "58abeeaebe89fa5e65bae305f5325a13"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "ba349abd7370252215ebf9e2f246283c"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "c91ff30df7644c3fd5be1355533d9fef"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "04d025e1102bede70d0aa9dc25a89e01"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "a1fcce758ed1bd8ead5030b598fd66eb"});
final String NA12878bandedResolutionMD5 = "87900cbed775471f1a7ad6582b0581f9";
final String NA12878bandedResolutionMD5 = "12ce2c83d71ad3db7269c22e65a47ffb";
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5});
tests.add(new Object[]{NA12878_WEx + " -I " + privateTestDir + "NA20313.highCoverageRegion.bam -sn NA12878",
ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5});
@ -116,12 +116,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
// 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, "254b4bed7fc8ef5d3c4cb4ebf4ea73c2"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "3f9e2b721c3bc8a6d76aa75bb7544f28"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "bfd12d811446cde2466508033cae7122"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "8e35def5c821afa9b6fbeed0aed0a866"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "8cebba1996a2aca29370c4d85f12128c"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "8abc60102776b34e22858ca157c784a9"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "e85d74be34c91ab84ea1e6ab6276fbab"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "10dd974f0fd83b8f187e1e9f39ba9237"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "fc7ae67b25ff3e82062b80827bd30f6d"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "87a745384652813976ee37091be45a14"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "a36a9f819e82f7ba6d77ab0b65475fbc"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "bbd62dbeddfdc7353264870e4379cc04"});
return tests.toArray(new Object[][]{});
}
@ -134,19 +134,19 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
// 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, "d8daf60c68f39875680cc037f264ccc0"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "dd1e6ee5e242fa1caa7f64a9605e4b16"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "a040bb2ebacf5afab3490504730043a1"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "d5ed4c847250a1096b6a5a2eac61d8dc"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "0d41cee1d7bd3c6df9816cc87a8a9d7c"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "f8775dd95c3b185fc6abdb3ef8da3833"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "7f1b295150967269545096564d5ebcca"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "97c5a77752305990420d5d725c70c2cd"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "04b5f3f7a6d1c53beef14c8b295883b1"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "f0b3e472e175ffa4fdf4e04f88e0ade1"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "747204e4bad4620c5298b683813c65ee"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "5a2d32868f007d9d3537ee9d66bd6f38"});
return tests.toArray(new Object[][]{});
}
/**
* Example testng test using MyDataProvider
* Test HaplotypeCaller, using MyDataProvider
*/
@Test(dataProvider = "MyDataProvider")
public void testHCWithGVCF(String bam, ReferenceConfidenceMode mode, String intervals, String md5) {
@ -158,7 +158,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
}
/**
* Example testng test using MyDataProvider
* Test HaplotypeCaller with haploid samples, using MyDataProviderHaploid
*/
@Test(dataProvider = "MyDataProviderHaploid", enabled=true)
public void testHCWithGVCFHaploid(final String bam, final ReferenceConfidenceMode mode, final String intervals, final String md5) {
@ -170,7 +170,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
}
/**
* Example testng test using MyDataProvider
* Test HaplotypeCaller with tetraploid samples, using MyDataProviderTetraploid
*/
@Test(dataProvider = "MyDataProviderTetraploid", enabled=true)
public void testHCWithGVCFTetraploid(final String bam, final ReferenceConfidenceMode mode, final String intervals, final String md5) {
@ -182,7 +182,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
}
/**
* Example testng test using MyDataProvider
* Test HaplotypeCaller with manyploid samples, using MyDataProviderManyploid
*/
@Test(dataProvider = "MyDataProviderManyploid", enabled=true)
public void testHCWithGVCFManyploid(final String bam, final ReferenceConfidenceMode mode, final String intervals, final String md5) {
@ -241,7 +241,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
public void testWrongGVCFNonVariantRecordOrderBugFix() {
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, WRONG_GVCF_RECORD_ORDER_BUGFIX_BAM, WRONG_GVCF_RECORD_ORDER_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9961c55d50332b61c9084fae2b256856"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("ae90a1b5c40f19df38e8ac58c3844ed5"));
spec.disableShadowBCF();
executeTest("testMissingGVCFIndexingStrategyException", spec);
}
@ -258,7 +258,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
public void testNoCallGVCFMissingPLsBugFix() {
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, NOCALL_GVCF_BUGFIX_BAM, NOCALL_GVCF_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("a376680db27c907c6acd0e07bbde8f92"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("bf6325fbc06c80893f3170668cfbed06"));
spec.disableShadowBCF();
executeTest("testNoCallGVCFMissingPLsBugFix", spec);
}

99
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -56,6 +56,8 @@ import htsjdk.tribble.readers.LineIterator;
import htsjdk.tribble.readers.PositionalBufferedStream;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFCodec;
import htsjdk.variant.vcf.VCFConstants;
import org.apache.commons.io.FileUtils;
import org.broadinstitute.gatk.engine.walkers.WalkerTest;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.GenomeLocParser;
@ -85,95 +87,96 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
final static String HMM_SUB_IMPLEMENTATION = "UNVECTORIZED";
final static String ALWAYS_LOAD_VECTOR_HMM = "-alwaysloadVectorHMM";
private void HCTest(String bam, String args, String md5) {
private void HCTest(String bam, String args, String md5) throws IOException {
final String base = String.format("-T HaplotypeCaller --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE --maxReadsInRegionPerSample 1000 --minReadsPerAlignmentStart 5 --maxProbPropagationDistance 50 --activeProbabilityThreshold 0.002 -pairHMMSub %s %s -R %s -I %s -L %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, bam, INTERVALS_FILE) + " --no_cmdline_in_header -o %s -minPruning 3";
final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
executeTest("testHaplotypeCaller: args=" + args, spec);
final File outputVCF = executeTest("testHaplotypeCaller: args=" + args, spec).getFirst().get(0);
Assert.assertFalse(FileUtils.readFileToString(outputVCF).contains(VCFConstants.MAPPING_QUALITY_ZERO_KEY));
}
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "9863e997c4f4be60e7e76a5573ec270f");
public void testHaplotypeCallerMultiSample() throws IOException {
HCTest(CEUTRIO_BAM, "", "6d8a38310a086f4d80f25d2b80a309b2");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "e85ada8486a4ed7231918187a100e1c3");
public void testHaplotypeCallerSingleSample() throws IOException {
HCTest(NA12878_BAM, "", "93990d0fed73087294548e71c4e661e9");
}
@Test
public void testHaplotypeCallerMultiSampleHaploid() {
HCTest(CEUTRIO_BAM,
"-ploidy 1", "1adc1d54b9d0cd493d85c6406ae4d4a7");
public void testHaplotypeCallerMultiSampleHaploid() throws IOException {
HCTest(CEUTRIO_BAM, "-ploidy 1", "deac83402aa9ef26fcc42e5ab08140d3");
}
@Test
public void testHaplotypeCallerSingleSampleHaploid() {
HCTest(NA12878_BAM, "-ploidy 1", "e5c8a8bfb4d9d522e610a2299a9b32ad");
public void testHaplotypeCallerSingleSampleHaploid() throws IOException {
HCTest(NA12878_BAM, "-ploidy 1", "633d7bd09d202b062854a647ec0f3ce0");
}
@Test
public void testHaplotypeCallerSingleSampleTetraploid() {
HCTest(NA12878_BAM, "-ploidy 4", "af711f92b33d3f42e87a719745d93a68");
public void testHaplotypeCallerSingleSampleTetraploid() throws IOException {
HCTest(NA12878_BAM, "-ploidy 4", "605498f14cb0b01695109035068a147e");
}
@Test
public void testHaplotypeCallerMinBaseQuality() {
HCTest(NA12878_BAM, "-mbq 15", "e85ada8486a4ed7231918187a100e1c3");
public void testHaplotypeCallerMinBaseQuality() throws IOException {
HCTest(NA12878_BAM, "-mbq 15", "93990d0fed73087294548e71c4e661e9");
}
@Test
public void testHaplotypeCallerMinBaseQualityHaploid() {
HCTest(NA12878_BAM, "-mbq 15 -ploidy 1", "e5c8a8bfb4d9d522e610a2299a9b32ad");
public void testHaplotypeCallerMinBaseQualityHaploid() throws IOException {
HCTest(NA12878_BAM, "-mbq 15 -ploidy 1", "633d7bd09d202b062854a647ec0f3ce0");
}
@Test
public void testHaplotypeCallerMinBaseQualityTetraploid() {
HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "af711f92b33d3f42e87a719745d93a68");
public void testHaplotypeCallerMinBaseQualityTetraploid() throws IOException {
HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "605498f14cb0b01695109035068a147e");
}
@Test
public void testHaplotypeCallerGraphBasedSingleSample() {
HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "129965453a3ad9a22aa241f8c4afcbbf");
public void testHaplotypeCallerGraphBasedSingleSample() throws IOException {
HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "1bd3336031e18c5f06abe760c33dd6be");
}
@Test
public void testHaplotypeCallerGraphBasedMultiSampleHaploid() {
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "1cf7e07f659c0aa462e17d2fe2981613");
public void testHaplotypeCallerGraphBasedMultiSampleHaploid() throws IOException {
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "e4a2b4c7adc7d45e2ad2bb61d263b9ac");
}
@Test
public void testHaplotypeCallerGraphBasedMultiSample() {
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "4d8fdb7ae9dd599f8c9f54ae4484ef38");
public void testHaplotypeCallerGraphBasedMultiSample() throws IOException {
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "dc757f57a6ddac88ddceab5be1533f89");
}
@Test
public void testHaplotypeCallerSingleSampleWithDbsnp() {
HCTest(NA12878_BAM, "-D " + b37dbSNP132, "0f9f45384669cde243731ca803fa3a0b");
public void testHaplotypeCallerSingleSampleWithDbsnp() throws IOException {
HCTest(NA12878_BAM, "-D " + b37dbSNP132, "c68a0659d6de9fb1c2f8e2db4da2f8a2");
}
@Test
public void testHaplotypeCallerMultiSampleGGA() {
public void testHaplotypeCallerMultiSampleGGA() throws IOException {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf" +
" -isr INTERSECTION -L " + GGA_INTERVALS_FILE,
"e9bc5ddd6e7e530268ffeee4c853f8f0");
"469228219a10f003e558aae66a838e73");
}
@Test
public void testHaplotypeCallerMultiSampleGGAHaploid() {
public void testHaplotypeCallerMultiSampleGGAHaploid() throws IOException {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -ploidy 1 -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -isr INTERSECTION -L 20:10080000-10100000",
"5c619c63de7ecf35b29562cf155ff5a0");
"535cde1cbefd5b90cae793cbbdce5893");
}
@Test
public void testHaplotypeCallerMultiSampleGGATetraploid() {
public void testHaplotypeCallerMultiSampleGGATetraploid() throws IOException {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -ploidy 4 -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -isr INTERSECTION -L 20:10080000-10100000",
"506f0b55414dbdb900c8705609f69d57");
"d8705ab5f7d4532c2ff8063244a72788");
}
@Test
public void testHaplotypeCallerInsertionOnEdgeOfContig() {
HCTest(CEUTRIO_MT_TEST_BAM, "-L MT:1-10", "455843da6331c282cb88943f25dafeec");
public void testHaplotypeCallerInsertionOnEdgeOfContig() throws IOException {
HCTest(CEUTRIO_MT_TEST_BAM, "-L MT:1-10", "60e578f65ab2be60f31ee8395845607a");
}
private void HCTestIndelQualityScores(String bam, String args, String md5) {
@ -184,7 +187,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "f2242d1696ef542196d363cf56159851");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "a139a6d01101064a4a093b24449d8b52");
}
private void HCTestNearbySmallIntervals(String bam, String args, String md5) {
@ -221,7 +224,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerNearbySmallIntervals() {
HCTestNearbySmallIntervals(NA12878_BAM, "", "e0794be1404bffd88738968e26b48cbb");
HCTestNearbySmallIntervals(NA12878_BAM, "", "f6fe463f338f6c5133ba08f1d667c23e");
}
// This problem bam came from a user on the forum and it spotted a problem where the ReadClipper
@ -231,14 +234,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void HCTestProblematicReadsModifiedInActiveRegions() {
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, 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("cf6fbb3636c52cd47dd14e0bd415a320"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("869e786baa1a72a08f0a3781804abb3e"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
}
@Test
public void HCTestStructuralIndels() {
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, 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("a145c3c0e99b278054a9960923da8aaa"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("1ca9a141cb65c6070a93d5a2c55a9b3b"));
executeTest("HCTestStructuralIndels: ", spec);
}
@ -293,7 +296,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestDBSNPAnnotationWGS() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
Arrays.asList("f0618b66e088b2d6fd831bb357de933c"));
Arrays.asList("2dc24f409ec1aa402ad892dffe317618"));
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
}
@ -302,7 +305,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,100,000-11,000,000 -D " + b37dbSNP132
+ " -L " + hg19Intervals + " -isr INTERSECTION", 1,
Arrays.asList("b279dfa0864495d0cbe45167c13d5a75"));
Arrays.asList("a2f40779558c1157353c6fcfd3783a76"));
executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
}
@ -310,7 +313,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestDBSNPAnnotationWGSGraphBased() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
Arrays.asList("1b15b696671a9da000d5ec0372f939a2"));
Arrays.asList("9d7ab1c89cce238cff055dc5e9091fb1"));
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
}
@ -319,7 +322,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-11,000,000 -D " + b37dbSNP132
+ " -L " + hg19Intervals + " -isr INTERSECTION", 1,
Arrays.asList("e46d99fb778e2aff09ccbbc1bda2a1bf"));
Arrays.asList("b2240a53e441064a1a60e60de4ca49ad"));
executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
}
@ -342,7 +345,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestAggressivePcrIndelModelWGS() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
Arrays.asList("32deea51cad0424bd8517fab3ad264ea"));
Arrays.asList("591f8f31524510ace882a860d6850871"));
executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec);
}
@ -350,7 +353,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestConservativePcrIndelModelWGS() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
Arrays.asList("04863dcc6f924b294814c9ef05d79a87"));
Arrays.asList("038db1cf0dadfe746a14e05f5cf3bb8e"));
executeTest("HC calling with conservative indel error modeling on WGS intervals", spec);
}
@ -370,7 +373,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void testLackSensitivityDueToBadHaplotypeSelectionFix() {
final String commandLine = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s -L %s --no_cmdline_in_header --maxNumHaplotypesInPopulation 16",
HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReferenceWithDecoy, privateTestDir + "hc-lack-sensitivity.bam", privateTestDir + "hc-lack-sensitivity.interval_list");
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9fa83f82ba63729edd8696e82bfeea49"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("e6bc4d979ae90c35809a2030ad709b5e"));
spec.disableShadowBCF();
executeTest("testLackSensitivityDueToBadHaplotypeSelectionFix", spec);
}
@ -379,7 +382,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void testMissingKeyAlternativeHaplotypesBugFix() {
final String commandLine = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s -L %s --no_cmdline_in_header ",
HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReferenceWithDecoy, privateTestDir + "lost-alt-key-hap.bam", privateTestDir + "lost-alt-key-hap.interval_list");
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("423b70c151a5d0028e104aa3372b8783"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("e8ef8b17a7561dd056805c15baec285e"));
spec.disableShadowBCF();
executeTest("testMissingKeyAlternativeHaplotypesBugFix", spec);
}
@ -402,7 +405,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
// but please make sure that both outputs get the same variant,
// alleles all with DBSNP ids
// We test here that change in active region size does not have an effect in placement of indels.
final String md5 = "8f572cfc1da9bdfc5e5725e092298ee6";
final String md5 = "df27ceb13e6cda2c97cacd23608c2f7f";
final WalkerTestSpec shortSpec = new WalkerTestSpec(commandLineShortInterval + " -o %s",Arrays.asList(md5));
executeTest("testDifferentIndelLocationsDueToSWExactDoubleComparisonsFix::shortInterval",shortSpec);
final WalkerTestSpec longSpec = new WalkerTestSpec(commandLineLongInterval + " -o %s",Arrays.asList(md5));