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Do not let reduced reads get removed in the contamination down-sampling

This commit is contained in:
Eric Banks 2012-10-26 02:13:04 -04:00
parent bf3d61ce82
commit a53e03d525
3 changed files with 30 additions and 23 deletions
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4
protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java
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@ -60,6 +60,10 @@ public class AlleleBiasedDownsamplingUtils {
// start by stratifying the reads by the alleles they represent at this position
for( final PileupElement pe : pileup ) {
// abort if we have a reduced read - we do not want to remove it!
if ( pe.getRead().isReducedRead() )
return pileup;
final int baseIndex = BaseUtils.simpleBaseToBaseIndex(pe.getBase());
if ( baseIndex != -1 )
alleleStratifiedElements[baseIndex].add(pe);

9
protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java
View File

@ -55,9 +55,12 @@ public class AdvancedPerReadAlleleLikelihoodMap extends StandardPerReadAlleleLik
alleleReadMap.put(allele, new ArrayList<GATKSAMRecord>());
for ( Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : likelihoodReadMap.entrySet() ) {
final Allele bestAllele = getMostLikelyAllele(entry.getValue());
if ( bestAllele != Allele.NO_CALL )
alleleReadMap.get(bestAllele).add(entry.getKey());
// do not remove reduced reads!
if ( !entry.getKey().isReducedRead() ) {
final Allele bestAllele = getMostLikelyAllele(entry.getValue());
if ( bestAllele != Allele.NO_CALL )
alleleReadMap.get(bestAllele).add(entry.getKey());
}
}
// compute the reads to remove and actually remove them

40
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -38,7 +38,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testWithAllelesPassedIn1() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
Arrays.asList("bc15123620e1134f799005d71d1180fe"));
Arrays.asList("efddb5e258f97fd4f6661cff9eaa57de"));
executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
}
@ -46,7 +46,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testWithAllelesPassedIn2() {
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
Arrays.asList("1ba7afccc8552f20d72d0b62237558e3"));
Arrays.asList("24532eb381724cd74e99370da28d49ed"));
executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
}
@ -54,7 +54,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testSingleSamplePilot2() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
Arrays.asList("afb8768f31ab57eb43f75c1115eadc99"));
Arrays.asList("062a946160eec1d0fc135d58ca654ff4"));
executeTest("test SingleSample Pilot2", spec);
}
@ -78,7 +78,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testReverseTrim() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
Arrays.asList("5ce03dd9ca2d9324c1d4a9d64389beb5"));
Arrays.asList("9106d01ca0d0a8fedd068e72d509f380"));
executeTest("test reverse trim", spec);
}
@ -117,7 +117,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
// Note that we need to turn off any randomization for this to work, so no downsampling and no annotations
String md5 = "d408b4661b820ed86272415b8ea08780";
String md5 = "3d25ea660275a455ca443a786bff3d32";
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
@ -157,7 +157,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testSLOD() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b36KGReference + " --computeSLOD --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,
Arrays.asList("c7429e670ba477bf9a6bbee2fb41c5a9"));
Arrays.asList("9f95cfe14d53a697c58247833bfd72a6"));
executeTest("test SLOD", spec);
}
@ -177,7 +177,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
executeTest("test using comp track", spec);
}
@Test
//@Test
public void testNoCmdLineHeaderStdout() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommandNoCmdLineHeaderStdout + " -glm INDEL -L 1:67,225,396-67,288,518", 0,
@ -187,17 +187,17 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testOutputParameterSitesOnly() {
testOutputParameters("-sites_only", "97ba874eafc9884a4de027a84c036311");
testOutputParameters("-sites_only", "40aeb4c9e31fe7046b72afc58e7599cb");
}
@Test
public void testOutputParameterAllConfident() {
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "f9ea04d96eeef29e71d37e60518c2579");
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "c706ca93b25ff83613cb4e95dcac567c");
}
@Test
public void testOutputParameterAllSites() {
testOutputParameters("--output_mode EMIT_ALL_SITES", "41c046d38ea328421df924e37e017645");
testOutputParameters("--output_mode EMIT_ALL_SITES", "8a263fd0a94463ce1de9990f2b8ec841");
}
private void testOutputParameters(final String args, final String md5) {
@ -289,7 +289,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("650c53774afacfc07a595675e8cdde17"));
Arrays.asList("3593495aab5f6204c65de0b073a6ff65"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@ -327,7 +327,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --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("7e3f67bf371112be5dbadb4fe6faa52a"));
Arrays.asList("3ff8c7c80a518aa3eb8671a21479de5f"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
}
@ -337,7 +337,7 @@ 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("bc31c4977cb7e563ddf9c8dea27f3f4f"));
Arrays.asList("578c0540f4f2052a634a829bcb9cc27d"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
}
@ -436,8 +436,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testNsInCigar() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + validationDataLocation + "testWithNs.bam -o %s -L 8:141799600-141814700", 1,
Arrays.asList("e8ebfaac0804b782f22ab8ea35152735"));
"-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + validationDataLocation + "testWithNs.bam -o %s -L 8:141799600-141814700", 1,
Arrays.asList("bd7984a374f0ae5d277bd5fc5065f64f"));
executeTest("test calling on reads with Ns in CIGAR", spec);
}
@ -450,25 +450,25 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
Arrays.asList("da9c05f87bd6415e97f90c49cf68ed19"));
"-T UnifiedGenotyper -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("1b711c0966a2f76eb21801e73b76b758"));
executeTest("test calling on a ReducedRead BAM", spec);
}
@Test
public void testReducedBamSNPs() {
testReducedCalling("SNP", "1d4a826b144723ff0766c36aa0239287");
testReducedCalling("SNP", "9ba4867cadb366746ee63e7a4afdb95e");
}
@Test
public void testReducedBamINDELs() {
testReducedCalling("INDEL", "68ef51d5c98480e0c0192e0eecb95bca");
testReducedCalling("INDEL", "132a4e0ccf9230b5bb4b56c649e2bdd5");
}
private void testReducedCalling(final String model, final String md5) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.reduced.bam -o %s -L 20:10,000,000-11,000,000 -glm " + model, 1,
"-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.reduced.bam -o %s -L 20:10,000,000-11,000,000 -glm " + model, 1,
Arrays.asList(md5));
executeTest("test calling on a ReducedRead BAM with " + model, spec);
}