FisherStrand now uses RankSumTest isUsableBase to decide if a read should be included in testing
-- Previously used hardcoded MAPQ > 20 && QUAL > 20 but now uses isUsableBase -- Updating MD5s as appropriate
This commit is contained in:
Mark DePristo
parent
30f441d385
commit
74e153ff4a
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@ -39,7 +39,7 @@ public class PoolCallerIntegrationTest extends WalkerTest {
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@Test
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public void testBOTH_GGA_Pools() {
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PC_LSV_Test(String.format(" -maxAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","POOLBOTH","da85bf56eeafae31b5a269b4e19b5db6");
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PC_LSV_Test(String.format(" -maxAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","POOLBOTH","36b8db57f65be1cc3d2d9d7f9f3f26e4");
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}
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@Test
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@ -49,13 +49,13 @@ public class PoolCallerIntegrationTest extends WalkerTest {
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@Test
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public void testMT_SNP_DISCOVERY_sp4() {
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PC_MT_Test(CEUTRIO_BAM, " -maxAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","060f06987a33f60433b0382cd7227140");
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PC_MT_Test(CEUTRIO_BAM, " -maxAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","fa5ee7c957c473a80f3a7f3c35dc80b5");
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}
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@Test
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public void testMT_SNP_GGA_sp10() {
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PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "df3ffc5cb76224ba152f543925eb3974");
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PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "6907c8617d49bb57b33f8704ce7f0323");
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}
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}
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@ -255,7 +255,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
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for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
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for (PileupElement p : sample.getValue().getBasePileup()) {
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if ( p.isDeletion() || p.getRead().isReducedRead() ) // ignore deletions and reduced reads
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if ( ! RankSumTest.isUsableBase(p, false) || p.getRead().isReducedRead() ) // ignore deletions and reduced reads
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continue;
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Allele base = Allele.create(p.getBase(), false);
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@ -298,9 +298,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
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final ReadBackedPileup pileup = context.getBasePileup();
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for ( final PileupElement p : pileup ) {
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if ( p.getRead().isReducedRead() ) // ignore reduced reads
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continue;
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if ( p.getRead().getMappingQuality() < 20 )
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if ( ! RankSumTest.isUsableBase(p, true) || p.getRead().isReducedRead() ) // ignore reduced reads
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continue;
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if ( indelLikelihoodMap.containsKey(p) ) {
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// to classify a pileup element as ref or alt, we look at the likelihood associated with the allele associated to this element.
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@ -149,9 +149,28 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements ActiveR
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protected abstract void fillIndelQualsFromPileup(final ReadBackedPileup pileup, final List<Double> refQuals, final List<Double> altQuals);
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protected static boolean isUsableBase(final PileupElement p) {
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/**
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* Can the base in this pileup element be used in comparative tests between ref / alt bases?
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*
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* Note that this function by default does not allow deletion pileup elements
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*
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* @param p the pileup element to consider
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* @return true if this base is part of a meaningful read for comparison, false otherwise
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*/
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public static boolean isUsableBase(final PileupElement p) {
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return isUsableBase(p, false);
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}
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/**
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* Can the base in this pileup element be used in comparative tests between ref / alt bases?
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*
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* @param p the pileup element to consider
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* @param allowDeletions if true, allow p to be a deletion base
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* @return true if this base is part of a meaningful read for comparison, false otherwise
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*/
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public static boolean isUsableBase(final PileupElement p, final boolean allowDeletions) {
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return !(p.isInsertionAtBeginningOfRead() ||
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p.isDeletion() ||
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(! allowDeletions && p.isDeletion()) ||
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p.getMappingQual() == 0 ||
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p.getMappingQual() == QualityUtils.MAPPING_QUALITY_UNAVAILABLE ||
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((int) p.getQual()) < QualityUtils.MIN_USABLE_Q_SCORE); // need the unBAQed quality score here
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@ -32,7 +32,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testHasAnnotsAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("e0a08416249515ea18bd0663c90c9330"));
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Arrays.asList("95b0627bfcac2191aed9908904e892ff"));
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executeTest("test file has annotations, asking for annotations, #1", spec);
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}
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@ -40,7 +40,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testHasAnnotsAsking2() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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Arrays.asList("0b60da46ba0eabb3abe5e0288937f9b0"));
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Arrays.asList("0e2509349fd6c8a9e9408c918215e1de"));
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executeTest("test file has annotations, asking for annotations, #2", spec);
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}
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@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoAnnotsAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("5eb576d0234c912d8efea184492691d0"));
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Arrays.asList("32d81a7797605afb526983a2ab45efc2"));
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executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
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}
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@ -74,7 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoAnnotsAsking2() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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Arrays.asList("8860524d793d24b2e32f318433fcf527"));
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Arrays.asList("350539ccecea0d1f7fffd4ac29c015e7"));
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executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
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}
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@ -90,7 +90,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testOverwritingHeader() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
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Arrays.asList("ebbf32f5b8b8d22f2eb247a0a3db3da0"));
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Arrays.asList("c222361819fae035a0162f876990fdee"));
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executeTest("test overwriting header", spec);
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}
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@ -28,7 +28,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMultiSamplePilot1() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
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Arrays.asList("f98c38defc8d619609399b4a3ba874e8"));
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Arrays.asList("0039fd0464c87e6ce66c4c8670fd8dfa"));
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executeTest("test MultiSample Pilot1", spec);
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}
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@ -52,7 +52,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testSingleSamplePilot2() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
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Arrays.asList("736607ee529b5624a3ab5521ab9e1b35"));
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Arrays.asList("61007c22c00a2871237280914a8f88f0"));
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executeTest("test SingleSample Pilot2", spec);
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}
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@ -60,7 +60,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMultipleSNPAlleles() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
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Arrays.asList("f33507add5d5c30448948906467dd3f3"));
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Arrays.asList("feda4a38bba096f7b740a146055509c2"));
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executeTest("test Multiple SNP alleles", spec);
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}
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@ -76,7 +76,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testReverseTrim() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
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Arrays.asList("0d724551e00129730b95fd4d70faaa58"));
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Arrays.asList("0ff525e65c5836289c454c76ead5d80e"));
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executeTest("test reverse trim", spec);
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}
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@ -86,7 +86,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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//
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// --------------------------------------------------------------------------------------------------------------
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private final static String COMPRESSED_OUTPUT_MD5 = "fe3429b736c50bb770e40c0320d498ed";
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private final static String COMPRESSED_OUTPUT_MD5 = "e1a17f8f852c3d639f26e659d37bc1e5";
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@Test
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public void testCompressedOutput() {
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@ -139,7 +139,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMinBaseQualityScore() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --min_base_quality_score 26", 1,
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Arrays.asList("b341b87742848a3224115fe94e73f244"));
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Arrays.asList("b0b92abbaaa4c787dce6f1b302f983ee"));
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executeTest("test min_base_quality_score 26", spec);
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}
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@ -147,7 +147,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testSLOD() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
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Arrays.asList("acb5332a267927d78edd51d93685111c"));
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Arrays.asList("186d33429756c89aad6cd89424d6dc94"));
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executeTest("test SLOD", spec);
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}
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@ -155,7 +155,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testNDA() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommand + " --annotateNDA -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
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Arrays.asList("74779b59730962bdf36a7a8ef84ac24d"));
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Arrays.asList("11b87f68b8530da168c1418513115f30"));
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executeTest("test NDA", spec);
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}
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@ -163,23 +163,23 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testCompTrack() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
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Arrays.asList("036edf58a4ed6c626f53bd2ab34b9f97"));
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Arrays.asList("d2be4b1af1f29579c4f96c08e1ddd871"));
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executeTest("test using comp track", spec);
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}
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@Test
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public void testOutputParameterSitesOnly() {
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testOutputParameters("-sites_only", "52b8336f347d182c158e8384b78f5a6d");
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testOutputParameters("-sites_only", "0055bd060e6ef53a6b836903d68953c9");
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}
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@Test
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public void testOutputParameterAllConfident() {
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testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "281363e6afb3260143bfdb22710e3d0e");
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testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "235bec0a7b2d901442261104db18f5eb");
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}
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@Test
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public void testOutputParameterAllSites() {
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testOutputParameters("--output_mode EMIT_ALL_SITES", "a802b672850b6fbc2764611d3ad071d9");
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testOutputParameters("--output_mode EMIT_ALL_SITES", "7c57ede7019063c19aa9d2136045d84f");
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}
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private void testOutputParameters(final String args, final String md5) {
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@ -193,7 +193,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testConfidence() {
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WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
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Arrays.asList("99ef7ba1747c7289ce1f963130539e18"));
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Arrays.asList("3f8d724a5158adac4df38c4e2ed04167"));
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executeTest("test confidence 1", spec1);
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}
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@ -201,7 +201,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testConfidence2() {
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WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1,
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Arrays.asList("99ef7ba1747c7289ce1f963130539e18"));
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Arrays.asList("3f8d724a5158adac4df38c4e2ed04167"));
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executeTest("test confidence 2", spec2);
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}
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@ -212,12 +212,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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// --------------------------------------------------------------------------------------------------------------
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@Test
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public void testHeterozyosity1() {
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testHeterozosity( 0.01, "7e1681b9052e357ca4a065fa76c8afb6" );
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testHeterozosity( 0.01, "7e7384a3a52e19f76f368c2f4561d510" );
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}
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@Test
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public void testHeterozyosity2() {
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testHeterozosity( 1.0 / 1850, "68a12f3eccac6cf4b27b6424f23628ee" );
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testHeterozosity( 1.0 / 1850, "3d16366d870c086e894c07c9da411795" );
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}
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private void testHeterozosity(final double arg, final String md5) {
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@ -241,7 +241,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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" -o %s" +
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" -L 1:10,000,000-10,100,000",
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1,
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Arrays.asList("b098a7744a448cf91a50886e4cc7d268"));
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Arrays.asList("58abc4f504d3afd42271e290ac846c4b"));
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executeTest(String.format("test multiple technologies"), spec);
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}
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@ -260,7 +260,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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" -L 1:10,000,000-10,100,000" +
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" -baq CALCULATE_AS_NECESSARY",
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1,
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Arrays.asList("2f008169b82d542ec9cc94908c395a0f"));
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Arrays.asList("e247f579f01eb698cfa1ae1e8a3995a8"));
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executeTest(String.format("test calling with BAQ"), spec);
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}
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@ -279,7 +279,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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" -o %s" +
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" -L 1:10,000,000-10,500,000",
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1,
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Arrays.asList("0d4177d7f963f4b4e8568613e7a468f0"));
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Arrays.asList("cc2167dce156f70f5a31ac3dce499266"));
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executeTest(String.format("test indel caller in SLX"), spec);
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}
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@ -307,7 +307,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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" -o %s" +
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" -L 1:10,000,000-10,500,000",
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1,
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Arrays.asList("181c4ed8dd084b83f8de92123bb85c41"));
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Arrays.asList("10c86ff98ad5ab800d208b435bcfbd7d"));
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executeTest(String.format("test indel calling, multiple technologies"), spec);
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}
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@ -317,7 +317,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
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"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
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Arrays.asList("5250cefb1fff262a6a3985dee29c154d"));
|
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Arrays.asList("c0c4dbb050296633a3150b104b77e05a"));
|
||||
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
|
||||
}
|
||||
|
||||
|
|
@ -327,7 +327,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
|
||||
+ privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
|
||||
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
|
||||
Arrays.asList("ebba1c06555c469cfb01d87f34aa6783"));
|
||||
Arrays.asList("2472722f87f8718861698f60bbba2462"));
|
||||
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
|
||||
}
|
||||
|
||||
|
|
@ -335,7 +335,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testMultiSampleIndels1() {
|
||||
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
|
||||
baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
|
||||
Arrays.asList("01fd223deb4f88fb7d9ee9736b664d8a"));
|
||||
Arrays.asList("eeb64b261f0a44aa478d753dbbf9378e"));
|
||||
List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
|
||||
|
||||
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
|
||||
|
|
@ -384,7 +384,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testMinIndelFraction0() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
assessMinIndelFraction + " -minIndelFrac 0.0", 1,
|
||||
Arrays.asList("25465c6dd3c4845f61b0f8e383388824"));
|
||||
Arrays.asList("160600dfa8e46f91dbb5d574517aac74"));
|
||||
executeTest("test minIndelFraction 0.0", spec);
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue