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Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ami Levy Moonshine 2012-10-18 14:49:34 -04:00
parent f665c6ceb9 b4e69239dd
commit a0381f15af
7 changed files with 35 additions and 33 deletions
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4
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
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@ -70,12 +70,12 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","7d6f319b9edcb1ff8c290fef150a2df8");
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","9acfe0019efdc91217ee070acb071228");
}
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","dd02890123e07e7412a49475cb6280f1");
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","c1d4dd793f61710a1b1fc5d82803210f");
}
@Test(enabled = true)

4
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -21,7 +21,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "8c52c0955099cca3215a0d78fd455894");
HCTest(CEUTRIO_BAM, "", "75013fa6a884104f0b1797502b636698");
}
@Test
@ -31,7 +31,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles_for_indels 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "61c1a0fb62d909229af6b5a91dad8b35");
HCTest(CEUTRIO_BAM, "--max_alternate_alleles_for_indels 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "3cd3363976b1937d801f9f82996f4abe");
}
private void HCTestComplexVariants(String bam, String args, String md5) {

14
public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
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@ -157,18 +157,22 @@ public abstract class MicroScheduler implements MicroSchedulerMBean {
if ( ! (walker instanceof TreeReducible) ) {
throw badNT("nt", engine, walker);
} else {
return new HierarchicalMicroScheduler(engine, walker, reads, reference, rods, threadAllocation);
}
}
if ( threadAllocation.getNumCPUThreadsPerDataThread() > 1 && ! (walker instanceof NanoSchedulable) ) {
throw badNT("nct", engine, walker);
}
if ( threadAllocation.getNumDataThreads() > 1 ) {
return new HierarchicalMicroScheduler(engine, walker, reads, reference, rods, threadAllocation);
} else {
if ( threadAllocation.getNumCPUThreadsPerDataThread() > 1 && ! (walker instanceof NanoSchedulable) )
throw badNT("nct", engine, walker);
return new LinearMicroScheduler(engine, walker, reads, reference, rods, threadAllocation);
}
}
private static UserException badNT(final String parallelArg, final GenomeAnalysisEngine engine, final Walker walker) {
throw new UserException.BadArgumentValue("nt",
throw new UserException.BadArgumentValue(parallelArg,
String.format("The analysis %s currently does not support parallel execution with %s. " +
"Please run your analysis without the %s option.", engine.getWalkerName(walker.getClass()), parallelArg, parallelArg));
}

4
public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
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@ -123,13 +123,13 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
// This parser has been passed a null filename and the GATK is not responsible for creating a type default for the object;
// therefore, the user must have failed to specify a type default
if(writerFileName.asFile() == null && generateMD5)
if(writerFileName != null && writerFileName.asFile() == null && generateMD5)
throw new ArgumentException("MD5 generation specified, but no output file specified. If md5 generation is desired, please specify a BAM output file and an md5 file will be written alongside.");
// Create the stub and set parameters.
SAMFileWriterStub stub = null; // stub = new SAMFileWriterStub(engine, defaultOutputStream);
if ( writerFileName.asFile() != null ) {
if (writerFileName != null && writerFileName.asFile() != null ) {
stub = new SAMFileWriterStub(engine, writerFileName.asFile());
if ( compressionLevel != null )

19
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PerReadAlleleLikelihoodMap.java
View File

@ -113,23 +113,20 @@ public class PerReadAlleleLikelihoodMap {
return likelihoodReadMap.get(p.getRead());
}
public static Allele getMostLikelyAllele(Map<Allele,Double> alleleMap) {
double minLike = Double.POSITIVE_INFINITY, maxLike = Double.NEGATIVE_INFINITY;
public static Allele getMostLikelyAllele( final Map<Allele,Double> alleleMap ) {
double maxLike = Double.NEGATIVE_INFINITY;
double prevMaxLike = Double.NEGATIVE_INFINITY;
Allele mostLikelyAllele = Allele.NO_CALL;
for (Map.Entry<Allele,Double> el : alleleMap.entrySet()) {
for (final Map.Entry<Allele,Double> el : alleleMap.entrySet()) {
if (el.getValue() > maxLike) {
prevMaxLike = maxLike;
maxLike = el.getValue();
mostLikelyAllele = el.getKey();
} else if( el.getValue() > prevMaxLike ) {
prevMaxLike = el.getValue();
}
if (el.getValue() < minLike)
minLike = el.getValue();
}
if (maxLike-minLike > INDEL_LIKELIHOOD_THRESH)
return mostLikelyAllele;
else
return Allele.NO_CALL;
return (maxLike - prevMaxLike > INDEL_LIKELIHOOD_THRESH ? mostLikelyAllele : Allele.NO_CALL );
}
}

12
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -42,11 +42,11 @@ import org.broadinstitute.sting.utils.MendelianViolation;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import java.io.File;
import java.io.FileNotFoundException;
@ -542,9 +542,11 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
VariantContext sub = subsetRecord(vc, EXCLUDE_NON_VARIANTS);
if ( REGENOTYPE && sub.isPolymorphicInSamples() && hasPLs(sub) ) {
final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(sub)).filters(sub.getFiltersMaybeNull());
addAnnotations(builder, sub);
sub = builder.make();
synchronized (UG_engine) {
final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(sub)).filters(sub.getFiltersMaybeNull());
addAnnotations(builder, sub);
sub = builder.make();
}
}
if ( (!EXCLUDE_NON_VARIANTS || sub.isPolymorphicInSamples()) && (!EXCLUDE_FILTERED || !sub.isFiltered()) ) {

11
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -60,7 +60,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultipleSNPAlleles() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-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,
Arrays.asList("26af30187316f742878c85f0ed091837"));
Arrays.asList("48b4f4b05461be276bffc91350f08cbc"));
executeTest("test Multiple SNP alleles", spec);
}
@ -76,7 +76,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testReverseTrim() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-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,
Arrays.asList("aa9cf96ab8f5aa844387e3aef1f27249"));
Arrays.asList("04affcc9d720ee17bc221759707e0cd2"));
executeTest("test reverse trim", spec);
}
@ -84,7 +84,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMismatchedPLs() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
Arrays.asList("d210ee1baa75dd4a0c63aef6b1fa7a8a"));
Arrays.asList("112e7bedfd284d4d9390aa006118c733"));
executeTest("test mismatched PLs", spec);
}
@ -343,13 +343,13 @@ 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("7fc488fe16dea9f023bfcfdaa908a548"));
Arrays.asList("863ee56b3594f09795644127f2f9539f"));
List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
"low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
Arrays.asList("f3ff7fe0f15f31eadd726c711d6bf3de"));
Arrays.asList("503ca1b75cc7b2679eaa80f7b5e7ef1c"));
executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
}
@ -452,5 +452,4 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
Arrays.asList("bbf16e1873e525ee5975021cfb8988cf"));
executeTest("test calling on a ReducedRead BAM", spec);
}
}