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Restore the read filter function in the HaplotypeCaller.

This commit is contained in:
Ryan Poplin 2013-04-16 09:37:04 -04:00
parent e176fc3af1
commit e0dfe5ca14
3 changed files with 17 additions and 16 deletions
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11
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -565,17 +565,18 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
// abort early if something is out of the acceptable range
if( assemblyResult.haplotypes.size() == 1 ) { return 1; } // only the reference haplotype remains so nothing else to do!
if( assemblyResult.regionForGenotyping.size() == 0 ) { return 1; } // no reads remain after filtering so nothing else to do!
if (dontGenotype) return 1; // user requested we not proceed
// evaluate each sample's reads against all haplotypes
//logger.info("Computing read likelihoods with " + assemblyResult.regionForGenotyping.size() + " reads");
final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = likelihoodCalculationEngine.computeReadLikelihoods( assemblyResult.haplotypes, splitReadsBySample( assemblyResult.regionForGenotyping.getReads() ) );
// filter out reads from genotyping which fail mapping quality based criteria
final List<GATKSAMRecord> filteredReads = filterNonPassingReads( assemblyResult.regionForGenotyping );
final Map<String, List<GATKSAMRecord>> perSampleFilteredReadList = splitReadsBySample( filteredReads );
if( assemblyResult.regionForGenotyping.size() == 0 ) { return 1; } // no reads remain after filtering so nothing else to do!
// evaluate each sample's reads against all haplotypes
//logger.info("Computing read likelihoods with " + assemblyResult.regionForGenotyping.size() + " reads");
final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = likelihoodCalculationEngine.computeReadLikelihoods( assemblyResult.haplotypes, splitReadsBySample( assemblyResult.regionForGenotyping.getReads() ) );
// subset down to only the best haplotypes to be genotyped in all samples ( in GGA mode use all discovered haplotypes )
final List<Haplotype> bestHaplotypes = selectBestHaplotypesForGenotyping(assemblyResult.haplotypes, stratifiedReadMap);

6
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
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@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleComplex1() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "a2a5ae267cc061b0f9148280c8f1e236");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "c0379d32c8c743d84c6da5956d67c004");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -88,12 +88,12 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleGGAComplex() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
"125e93deeb3b390a14d9b777aa2a220f");
"2fb56d241baca3658af5811e680bde4c");
}
@Test
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
"6957fd0e8a5bc66d2572a6ca8626fa7a");
"bd7d24e87776f939b36742c1fd33b25c");
}
}

16
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -80,12 +80,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "3d5e59b3a74da999ceb967cef73086b4");
HCTest(CEUTRIO_BAM, "", "943302eb9b9798d1ffeb9136612cbc85");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "4afef5e9cb99c0292e471d0c95243c1a");
HCTest(NA12878_BAM, "", "3199bebe4e34b5df7558f74b05fb3a4e");
}
@Test(enabled = false) // can't annotate the rsID's yet
@ -96,7 +96,7 @@ 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",
"d00a604abe02586f803b1bb9d63af0f7");
"aef51f79d58634e4b35a1a98caba329c");
}
@Test
@ -112,7 +112,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "4581b4c2b55b2290a4b1092d2da5e642");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "5ac0d4b30a0c9a97a71ad014e63f11cf");
}
private void HCTestNearbySmallIntervals(String bam, String args, String md5) {
@ -149,7 +149,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerNearbySmallIntervals() {
HCTestNearbySmallIntervals(NA12878_BAM, "", "b20aaef138ef21a5031c06434f17f685");
HCTestNearbySmallIntervals(NA12878_BAM, "", "a7e3b05fdc9866965e3ab71dbbd288ff");
}
// This problem bam came from a user on the forum and it spotted a problem where the ReadClipper
@ -166,7 +166,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@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("9bea757f6aa75e43585e26b246fd8897"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("8252f956e94cb8538b18210e9350f0e3"));
executeTest("HCTestStructuralIndels: ", spec);
}
@ -188,7 +188,7 @@ 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("a360a9e14c4e9c9b7435ca5d9dfadb8d"));
Arrays.asList("7d4da215e86658e8da70fa0ade7f3eca"));
executeTest("HC calling on a ReducedRead BAM", spec);
}
@ -196,7 +196,7 @@ 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("8adfa8a27a312760dab50787da595c57"));
Arrays.asList("b0f0467dd4bfc4cdc85fff85ffa6f0c1"));
executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec);
}
}