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This commit incorporates several different changes that each pretty much break all the VCF-based integration tests, so I bunched them all together. We now officially emit VCF4.1 files (woo hoo), which means that the VCF headers are now all different (header version is 4.1 plus counts for some of the annotations are 'A' or 'G'). Also, I've added a Read Filter for reads with MQ=255 ('unavailable' in the SAM spec) and have applied this to the UG and the RMS MQ annotation.

This commit is contained in:
Eric Banks 2011-07-12 14:11:53 -04:00
parent 329c3d8050
commit a2597e7f00
28 changed files with 169 additions and 119 deletions
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43
public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java 100644
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@ -0,0 +1,43 @@
/*
* Copyright (c) 2009 The Broad Institute
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.util.QualityUtil;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.QualityUtils;
/**
* Filter out mapping quality zero reads.
*
* @author ebanks
* @version 0.1
*/
public class MappingQualityUnavailableReadFilter extends ReadFilter {
public boolean filterOut(SAMRecord rec) {
return (rec.getMappingQuality() == QualityUtils.MAPPING_QUALITY_UNAVAILABLE);
}
}

5
public/java/src/org/broadinstitute/sting/gatk/filters/ZeroMappingQualityReadFilter.java → public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityZeroReadFilter.java
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@ -24,17 +24,16 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
/**
* Filter out zero mapping quality reads.
* Filter out mapping quality zero reads.
*
* @author hanna
* @version 0.1
*/
public class ZeroMappingQualityReadFilter extends ReadFilter {
public class MappingQualityZeroReadFilter extends ReadFilter {
public boolean filterOut(SAMRecord rec) {
return (rec.getMappingQuality() == 0);
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
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@ -62,5 +62,5 @@ public class AlleleBalanceBySample implements GenotypeAnnotation, ExperimentalAn
public List<String> getKeyNames() { return Arrays.asList("AB"); }
public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), -1, VCFHeaderLineType.Float, "Allele balance for each het genotype")); }
public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Allele balance for each het genotype")); }
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
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@ -42,8 +42,8 @@ import java.util.*;
public class ChromosomeCounts implements InfoFieldAnnotation, StandardAnnotation {
private String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY };
private VCFInfoHeaderLine[] descriptions = { new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"),
new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"),
private VCFInfoHeaderLine[] descriptions = { new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"),
new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"),
new VCFInfoHeaderLine(VCFConstants.ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of alleles in called genotypes") };
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {

7
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
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@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
@ -21,7 +22,7 @@ public class MappingQualityRankSumTest extends RankSumTest {
protected void fillQualsFromPileup(byte ref, byte alt, ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {
for ( final PileupElement p : pileup ) {
if( isUsableBase(p) && p.getMappingQual() < 254 ) { // 254 and 255 are special mapping qualities used as a code by aligners
if ( isUsableBase(p) ) {
if ( p.getBase() == ref ) {
refQuals.add((double)p.getMappingQual());
} else if ( p.getBase() == alt ) {
@ -34,7 +35,7 @@ public class MappingQualityRankSumTest extends RankSumTest {
// equivalent is whether indel likelihoods for reads corresponding to ref allele are more likely than reads corresponding to alt allele ?
HashMap<PileupElement,LinkedHashMap<Allele,Double>> indelLikelihoodMap = IndelGenotypeLikelihoodsCalculationModel.getIndelLikelihoodMap();
for (final PileupElement p: pileup) {
if (indelLikelihoodMap.containsKey(p) && p.getMappingQual() < 254) {
if (indelLikelihoodMap.containsKey(p) && p.getMappingQual() != 0 && p.getMappingQual() != QualityUtils.MAPPING_QUALITY_UNAVAILABLE) {
// retrieve likelihood information corresponding to this read
LinkedHashMap<Allele,Double> el = indelLikelihoodMap.get(p);
// by design, first element in LinkedHashMap was ref allele
@ -54,8 +55,6 @@ public class MappingQualityRankSumTest extends RankSumTest {
refQuals.add((double)p.getMappingQual());
else if (altLikelihood > refLikelihood + INDEL_LIKELIHOOD_THRESH)
altQuals.add((double)p.getMappingQual());
}
}
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
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@ -47,5 +47,5 @@ public class NBaseCount implements InfoFieldAnnotation {
public List<String> getKeyNames() { return Arrays.asList("PercentNBaseSolid"); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("PercentNBaseSolid", 4, VCFHeaderLineType.Float, "Percentage of N bases in the pileup (counting only SOLiD reads)")); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("PercentNBaseSolid", 1, VCFHeaderLineType.Float, "Percentage of N bases in the pileup (counting only SOLiD reads)")); }
}

7
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
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@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
@ -38,8 +39,10 @@ public class RMSMappingQuality implements InfoFieldAnnotation, StandardAnnotatio
pileup = context.getBasePileup();
if (pileup != null) {
for (PileupElement p : pileup )
qualities[index++] = p.getRead().getMappingQuality();
for (PileupElement p : pileup ) {
if ( p.getMappingQual() != QualityUtils.MAPPING_QUALITY_UNAVAILABLE )
qualities[index++] = p.getMappingQual();
}
}
}

5
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
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@ -106,6 +106,9 @@ public abstract class RankSumTest implements InfoFieldAnnotation, StandardAnnota
protected abstract void fillIndelQualsFromPileup(ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals);
protected static boolean isUsableBase( final PileupElement p ) {
return !( p.isDeletion() || p.getMappingQual() == 0 || ((int)p.getQual()) < 6 ); // need the unBAQed quality score here
return !( p.isDeletion() ||
p.getMappingQual() == 0 ||
p.getMappingQual() == QualityUtils.MAPPING_QUALITY_UNAVAILABLE ||
((int)p.getQual()) < QualityUtils.MIN_USABLE_Q_SCORE ); // need the unBAQed quality score here
}
}

5
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -25,6 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.gatk.contexts.*;
import org.broadinstitute.sting.gatk.filters.BadMateFilter;
@ -47,7 +48,7 @@ import java.io.PrintStream;
* multi-sample data. The user can choose from several different incorporated calculation models.
*/
@BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_INPUT)
@ReadFilters( {BadMateFilter.class} )
@ReadFilters( {BadMateFilter.class, MappingQualityUnavailableReadFilter.class} )
@Reference(window=@Window(start=-200,stop=200))
@By(DataSource.REFERENCE)
@Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250)
@ -175,7 +176,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Genotype Quality"));
result.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Read Depth (only filtered reads used for calling)"));
result.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Float, "Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; if site is not biallelic, number of likelihoods if n*(n+1)/2"));
result.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"));
return result;
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
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@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.filters.BadCigarFilter;
import org.broadinstitute.sting.gatk.filters.Platform454Filter;
import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
import org.broadinstitute.sting.gatk.filters.BadMateFilter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
@ -50,7 +50,7 @@ import java.io.PrintStream;
/**
* Emits intervals for the Local Indel Realigner to target for cleaning. Ignores 454 reads, MQ0 reads, and reads with consecutive indel operators in the CIGAR string.
*/
@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class, BadCigarFilter.class})
@ReadFilters({Platform454Filter.class, MappingQualityZeroReadFilter.class, BadCigarFilter.class})
@Reference(window=@Window(start=-1,stop=50))
@Allows(value={DataSource.READS, DataSource.REFERENCE})
@By(DataSource.REFERENCE)

2
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
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@ -72,7 +72,7 @@ import java.util.*;
* if first bam has coverage at the site but no indication for an indel. In the --somatic mode, BED output contains
* only somatic calls, while --verbose output contains all calls annotated with GERMLINE/SOMATIC keywords.
*/
@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class, PlatformUnitFilter.class})
@ReadFilters({Platform454Filter.class, MappingQualityZeroReadFilter.class, PlatformUnitFilter.class})
public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
// @Output
// PrintStream out;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
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@ -32,7 +32,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.datasources.sample.Sample;
import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.walkers.*;
@ -58,7 +58,7 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
@Requires(value = {DataSource.READS, DataSource.REFERENCE}, referenceMetaData = @RMD(name = "variant", type = ReferenceOrderedDatum.class))
@By(DataSource.READS)
@ReadFilters({ZeroMappingQualityReadFilter.class})
@ReadFilters({MappingQualityZeroReadFilter.class})
// Filter out all reads with zero mapping quality
public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, PhasingStats> {

4
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
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@ -34,7 +34,7 @@ import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.*;
@ -75,7 +75,7 @@ import java.util.Map;
@BAQMode(ApplicationTime = BAQ.ApplicationTime.FORBIDDEN)
@By( DataSource.READS ) // Only look at covered loci, not every loci of the reference file
@ReadFilters( {ZeroMappingQualityReadFilter.class} ) // Filter out all reads with zero mapping quality
@ReadFilters( {MappingQualityZeroReadFilter.class} ) // Filter out all reads with zero mapping quality
@Requires( {DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES} ) // This walker requires both -I input.bam and -R reference.fasta
@PartitionBy(PartitionType.LOCUS)
public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.CountedData, CountCovariatesWalker.CountedData> implements TreeReducible<CountCovariatesWalker.CountedData> {

4
public/java/src/org/broadinstitute/sting/utils/QualityUtils.java
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@ -9,9 +9,13 @@ import net.sf.samtools.SAMUtils;
* @author Kiran Garimella
*/
public class QualityUtils {
public final static byte MAX_QUAL_SCORE = SAMUtils.MAX_PHRED_SCORE;
public final static double MIN_REASONABLE_ERROR = 0.0001;
public final static byte MAX_REASONABLE_Q_SCORE = 40;
public final static byte MIN_USABLE_Q_SCORE = 6;
public final static int MAPPING_QUALITY_UNAVAILABLE = 255;
/**
* Private constructor. No instantiating this class!

6
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
View File

@ -123,12 +123,10 @@ public class StandardVCFWriter implements VCFWriter {
try {
// the file format field needs to be written first
mWriter.write(VCFHeader.METADATA_INDICATOR + VCFHeaderVersion.VCF4_0.getFormatString() + "=" + VCFHeaderVersion.VCF4_0.getVersionString() + "\n");
mWriter.write(VCFHeader.METADATA_INDICATOR + VCFHeaderVersion.VCF4_1.getFormatString() + "=" + VCFHeaderVersion.VCF4_1.getVersionString() + "\n");
for ( VCFHeaderLine line : mHeader.getMetaData() ) {
if ( line.getKey().equals(VCFHeaderVersion.VCF4_0.getFormatString()) ||
line.getKey().equals(VCFHeaderVersion.VCF3_3.getFormatString()) ||
line.getKey().equals(VCFHeaderVersion.VCF3_2.getFormatString()) )
if ( VCFHeaderVersion.isFormatString(line.getKey()) )
continue;
// are the records filtered (so we know what to put in the FILTER column of passing records) ?

28
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -15,7 +15,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsNotAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("4cc077eb3d343e6b7ba12bff86ebe347"));
Arrays.asList("8a105fa5eebdfffe7326bc5b3d8ffd1c"));
executeTest("test file has annotations, not asking for annotations, #1", spec);
}
@ -23,7 +23,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsNotAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("1de8e943fbf55246ebd19efa32f22a58"));
Arrays.asList("964f1016ec9a3c55333f62dd834c14d6"));
executeTest("test file has annotations, not asking for annotations, #2", spec);
}
@ -31,7 +31,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("93c110e45fd4aedb044a8a5501e23336"));
Arrays.asList("8e7de435105499cd71ffc099e268a83e"));
executeTest("test file has annotations, asking for annotations, #1", spec);
}
@ -39,7 +39,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("f5cb45910ed719f46159f9f71acaecf4"));
Arrays.asList("64b6804cb1e27826e3a47089349be581"));
executeTest("test file has annotations, asking for annotations, #2", spec);
}
@ -47,7 +47,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsNotAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("4b48e7d095ef73e3151542ea976ecd89"));
Arrays.asList("42ccee09fa9f8c58f4a0d4f1139c094f"));
executeTest("test file doesn't have annotations, not asking for annotations, #1", spec);
}
@ -55,7 +55,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsNotAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("28dfbfd178aca071b948cd3dc2365357"));
Arrays.asList("f2ddfa8105c290b1f34b7a261a02a1ac"));
executeTest("test file doesn't have annotations, not asking for annotations, #2", spec);
}
@ -63,7 +63,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("a330a5bc3ee72a51dbeb7e6c97a0db99"));
Arrays.asList("fd1ffb669800c2e07df1e2719aa38e49"));
executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
}
@ -71,7 +71,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("3a31d1ef471acfb881a2dec7963fe3f4"));
Arrays.asList("09f8e840770a9411ff77508e0ed0837f"));
executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
}
@ -79,7 +79,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testOverwritingHeader() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
Arrays.asList("a63fd8ff7bafbd46b7f009144a7c2ad1"));
Arrays.asList("78d2c19f8107d865970dbaf3e12edd92"));
executeTest("test overwriting header", spec);
}
@ -87,7 +87,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoReads() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
Arrays.asList("36378f1245bb99d902fbfe147605bc42"));
Arrays.asList("16e3a1403fc376320d7c69492cad9345"));
executeTest("not passing it any reads", spec);
}
@ -95,7 +95,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testDBTagWithDbsnp() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -D " + GATKDataLocation + "dbsnp_129_b36.rod -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
Arrays.asList("0257a1cc3c703535b2d3c5046bf88ab7"));
Arrays.asList("3da8ca2b6bdaf6e92d94a8c77a71313d"));
executeTest("getting DB tag with dbSNP", spec);
}
@ -103,7 +103,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testDBTagWithHapMap() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B:compH3,VCF " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
Arrays.asList("2d7c73489dcf0db433bebdf79a068764"));
Arrays.asList("1bc01c5b3bd0b7aef75230310c3ce688"));
executeTest("getting DB tag with HM3", spec);
}
@ -111,13 +111,13 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testUsingExpression() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B:foo,VCF " + validationDataLocation + "targetAnnotations.vcf -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variant", 1,
Arrays.asList("2f6efd08d818faa1eb0631844437c64a"));
Arrays.asList("e9c0d832dc6b4ed06c955060f830c140"));
executeTest("using expression", spec);
}
@Test
public void testTabixAnnotations() {
final String MD5 = "6c7a6a1c0027bf82656542a9b2671a35";
final String MD5 = "13269d5a2e16f06fd755cc0fb9271acf";
for ( String file : Arrays.asList("CEU.exon.2010_03.sites.vcf", "CEU.exon.2010_03.sites.vcf.gz")) {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -A HomopolymerRun -B:variant,VCF " + validationDataLocation + "/" + file + " -BTI variant -NO_HEADER", 1,

6
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java
View File

@ -29,7 +29,7 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
*/
String[] md5WithDashSArg = {"3d3b61a83c1189108eabb2df04218099"};
String[] md5WithDashSArg = {"efba4ce1641cfa2ef88a64395f2ebce8"};
WalkerTestSpec specWithSArg = new WalkerTestSpec(
"-T GenomicAnnotator -R " + b36KGReference +
" -B:variant,vcf3 /humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf" +
@ -58,7 +58,7 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("caa562160733aa638e1ba413ede209ae")
Arrays.asList("772fc3f43b70770ec6c6acbb8bbbd4c0")
);
executeTest("testGenomicAnnotatorOnIndels", testOnIndels);
}
@ -76,7 +76,7 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("a4cf76f08fa90284b6988a464b6e0c17")
Arrays.asList("081ade7f3d2d3c5f19cb1e8651a626f3")
);
executeTest("testGenomicAnnotatorOnSNPsAndIndels", testOnSNPsAndIndels);
}

6
public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
View File

@ -41,7 +41,7 @@ public class BeagleIntegrationTest extends WalkerTest {
"-B:beagleR2,BEAGLE " + beagleValidationDataLocation + "inttestbgl.r2 " +
"-B:beagleProbs,BEAGLE " + beagleValidationDataLocation + "inttestbgl.gprobs " +
"-B:beaglePhased,BEAGLE " + beagleValidationDataLocation + "inttestbgl.phased " +
"-o %s -NO_HEADER", 1, Arrays.asList("6bccee48ad2f06ba5a8c774fed444478"));
"-o %s -NO_HEADER", 1, Arrays.asList("3531451e84208264104040993889aaf4"));
executeTest("test BeagleOutputToVCF", spec);
}
@ -60,7 +60,7 @@ public class BeagleIntegrationTest extends WalkerTest {
"-T ProduceBeagleInput -B:variant,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878_HSQ_chr22_14-16m.vcf "+
"-B:validation,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878_OMNI_chr22_14-16m.vcf "+
"-L 22:14000000-16000000 -o %s -bvcf %s -bs 0.8 -valp 0.98 -R /humgen/1kg/reference/human_g1k_v37.fasta -NO_HEADER ",2,
Arrays.asList("660986891b30cdc937e0f2a3a5743faa","223fb977e8db567dcaf632c6ee51f294"));
Arrays.asList("660986891b30cdc937e0f2a3a5743faa","e96ddd51da9f4a797b2aa8c20e404166"));
executeTest("test BeagleInputWithBootstrap",spec);
}
@ -72,7 +72,7 @@ public class BeagleIntegrationTest extends WalkerTest {
"-B:beagleR2,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.r2 "+
"-B:beagleProbs,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.gprobs.bgl "+
"-B:beaglePhased,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.phased.bgl "+
"-L 20:1-70000 -o %s -NO_HEADER ",1,Arrays.asList("24b88ef8cdf6e347daab491f0256be5a"));
"-L 20:1-70000 -o %s -NO_HEADER ",1,Arrays.asList("8dd6ec53994fb46c5c22af8535d22965"));
executeTest("testBeagleChangesSitesToRef",spec);
}

22
public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
View File

@ -16,7 +16,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testNoAction() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("4cc077eb3d343e6b7ba12bff86ebe347"));
Arrays.asList("8a105fa5eebdfffe7326bc5b3d8ffd1c"));
executeTest("test no action", spec);
}
@ -24,7 +24,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testClusteredSnps() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -window 10 -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("ada5540bb3d9b6eb8f1337ba01e90a94"));
Arrays.asList("27b13f179bb4920615dff3a32730d845"));
executeTest("test clustered SNPs", spec);
}
@ -32,17 +32,17 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testMasks() {
WalkerTestSpec spec1 = new WalkerTestSpec(
baseTestString() + " -mask foo -B:mask,VCF3 " + validationDataLocation + "vcfexample2.vcf -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("b0fcac4af3526e3b2a37602ab4c0e6ae"));
Arrays.asList("578f9e774784c25871678e6464fd212b"));
executeTest("test mask all", spec1);
WalkerTestSpec spec2 = new WalkerTestSpec(
baseTestString() + " -mask foo -B:mask,VCF " + validationDataLocation + "vcfMask.vcf -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("b64baabe905a5d197cc1ab594147d3d5"));
Arrays.asList("bfa86a674aefca1b13d341cb14ab3c4f"));
executeTest("test mask some", spec2);
WalkerTestSpec spec3 = new WalkerTestSpec(
baseTestString() + " -mask foo -maskExtend 10 -B:mask,VCF " + validationDataLocation + "vcfMask.vcf -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("0eff92fe72024d535c44b98e1e9e1993"));
Arrays.asList("5939f80d14b32d88587373532d7b90e5"));
executeTest("test mask extend", spec3);
}
@ -50,7 +50,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testFilter1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("7a40795147cbfa92941489d7239aad92"));
Arrays.asList("45219dbcfb6f81bba2ea0c35f5bfd368"));
executeTest("test filter #1", spec);
}
@ -58,7 +58,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testFilter2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("e9dd4991b1e325847c77d053dfe8ee54"));
Arrays.asList("c95845e817da7352b9b72bc9794f18fb"));
executeTest("test filter #2", spec);
}
@ -66,7 +66,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testFilterWithSeparateNames() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("9ded2cce63b8d97550079047051d80a3"));
Arrays.asList("b8cdd7f44ff1a395e0a9b06a87e1e530"));
executeTest("test filter with separate names #2", spec);
}
@ -74,12 +74,12 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testGenotypeFilters() {
WalkerTestSpec spec1 = new WalkerTestSpec(
baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("6696e3f65a62ce912230d47cdb0c129b"));
Arrays.asList("96b61e4543a73fe725e433f007260039"));
executeTest("test genotype filter #1", spec1);
WalkerTestSpec spec2 = new WalkerTestSpec(
baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("26e5b4ee954c9e0b5eb044afd4b88ee9"));
Arrays.asList("6c8112ab17ce39c8022c891ae73bf38e"));
executeTest("test genotype filter #2", spec2);
}
@ -87,7 +87,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testDeletions() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --filterExpression 'QUAL < 100' --filterName foo -B:variant,VCF " + validationDataLocation + "twoDeletions.vcf", 1,
Arrays.asList("e63b58be33c9126ad6cc55489aac539b"));
Arrays.asList("569546fd798afa0e65c5b61b440d07ac"));
executeTest("test deletions", spec);
}
}

48
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -28,7 +28,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
Arrays.asList("258e1954e6ae55c89abc6a716e19cbe0"));
Arrays.asList("c97829259463d04b0159591bb6fb44af"));
executeTest("test MultiSample Pilot1", spec);
}
@ -54,12 +54,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testWithAllelesPassedIn() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
Arrays.asList("edeb1db288a24baff59575ceedd94243"));
Arrays.asList("2b69667f4770e8c0c894066b7f27e440"));
executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
Arrays.asList("581990130d90071b084024f4cd7caf91"));
Arrays.asList("b77fe007c2a97fcd59dfd5eef94d8b95"));
executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
}
@ -67,7 +67,7 @@ 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("d120db27d694a6da32367cc4fb5770fa"));
Arrays.asList("ee8a5e63ddd470726a749e69c0c20f60"));
executeTest("test SingleSample Pilot2", spec);
}
@ -77,7 +77,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
//
// --------------------------------------------------------------------------------------------------------------
private final static String COMPRESSED_OUTPUT_MD5 = "75e5c430ed39f79f24e375037a388dc4";
private final static String COMPRESSED_OUTPUT_MD5 = "ef31654a2b85b9b2d3bba4f4a75a17b6";
@Test
public void testCompressedOutput() {
@ -107,7 +107,7 @@ 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 = "a29615dd37222a11b8dadd341b53e43c";
String md5 = "46868a9c4134651c54535fb46b408aee";
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,
@ -138,9 +138,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testCallingParameters() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "--min_base_quality_score 26", "93e6269e38db9bc1732555e9969e3648" );
e.put( "--min_mapping_quality_score 26", "64be99183c100caed4aa5f8bad64c7e9" );
e.put( "--p_nonref_model GRID_SEARCH", "0592fe33f705ad8e2f13619fcf157805" );
e.put( "--min_base_quality_score 26", "5043c9a101e691602eb7a3f9704bdf20" );
e.put( "--min_mapping_quality_score 26", "71a833eb8fd93ee62ae0d5a430f27940" );
e.put( "--p_nonref_model GRID_SEARCH", "ddf443e9dcadef367476b26b4d52c134" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -153,9 +153,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testOutputParameter() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-sites_only", "1483e637dc0279935a7f90d136d147bb" );
e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "adcd91bc7dae8020df8caf1a30060e98" );
e.put( "--output_mode EMIT_ALL_SITES", "b708acc2fa40f336bcd2d0c70091e07e" );
e.put( "-sites_only", "eaad6ceb71ab94290650a70bea5ab951" );
e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "05bf7db8a3d19ef4a3d14772c90b732f" );
e.put( "--output_mode EMIT_ALL_SITES", "e4b86740468d7369f0156550855586c7" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -169,12 +169,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testConfidence() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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,
Arrays.asList("64be99183c100caed4aa5f8bad64c7e9"));
Arrays.asList("71a833eb8fd93ee62ae0d5a430f27940"));
executeTest("test confidence 1", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
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,
Arrays.asList("e76ca54232d02f0d92730e1affeb804e"));
Arrays.asList("79968844dc3ddecb97748c1acf2984c7"));
executeTest("test confidence 2", spec2);
}
@ -186,8 +186,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testHeterozyosity() {
HashMap<Double, String> e = new HashMap<Double, String>();
e.put( 0.01, "18d37f7f107853b5e32c757b4e143205" );
e.put( 1.0 / 1850, "2bcb90ce2f7542bf590f7612018fae8e" );
e.put( 0.01, "4e878664f61d2d800146d3762303fde1" );
e.put( 1.0 / 1850, "9204caec095ff5e63ca21a10b6fab453" );
for ( Map.Entry<Double, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -211,7 +211,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("825f05b31b5bb7e82231a15c7e4e2b0d"));
Arrays.asList("1a58ec52df545f946f80cc16c5736a91"));
executeTest(String.format("test multiple technologies"), spec);
}
@ -230,7 +230,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq CALCULATE_AS_NECESSARY",
1,
Arrays.asList("0919ab7e513c377610e23a67d33608fa"));
Arrays.asList("62d0f6d9de344ce68ce121c13b1e78b1"));
executeTest(String.format("test calling with BAQ"), spec);
}
@ -244,7 +244,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq OFF",
1,
Arrays.asList("825f05b31b5bb7e82231a15c7e4e2b0d"));
Arrays.asList("1a58ec52df545f946f80cc16c5736a91"));
executeTest(String.format("test calling with BAQ OFF"), spec);
}
@ -263,7 +263,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("cb37348c41b8181be829912730f747e1"));
Arrays.asList("631ae1f1eb6bc4c1a4136b8495250536"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@ -278,7 +278,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -minIndelCnt 1" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("ca5b6a5fb53ae401b146cc3044f454f2"));
Arrays.asList("fd556585c79e2b892a5976668f45aa43"));
executeTest(String.format("test indel caller in SLX witn low min allele count"), spec);
}
@ -291,7 +291,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("ca4343a4ab6d3cce94ce61d7d1910f81"));
Arrays.asList("9cd56feedd2787919e571383889fde70"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
@ -301,14 +301,14 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("3f555b53e9dd14cf7cdf96c24e322364"));
Arrays.asList("315e1b78d7a403d7fcbcf0caa8c496b8"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf "
+ validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("1b9764b783acf7822edc58e6822eef5b"));
Arrays.asList("cf89e0c54f14482a23c105b73a333d8a"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
}

12
public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
View File

@ -26,7 +26,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
+ " -L chr20:332341-382503",
1,
Arrays.asList("6020a68bbec97fcd87819c10cd4e2470"));
Arrays.asList("9568ba0b6624b97ac55a59bdee2d9150"));
executeTest("MAX 10 het sites [TEST ONE]; require PQ >= 10", spec);
}
@ -36,7 +36,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
+ " -L chr20:1232503-1332503",
1,
Arrays.asList("712c2145df4756c9a15758865d8007b5"));
Arrays.asList("ce65194c24fe83b0ec90faa6c8e6109a"));
executeTest("MAX 10 het sites [TEST TWO]; require PQ >= 10", spec);
}
@ -46,7 +46,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 2, 30)
+ " -L chr20:332341-382503",
1,
Arrays.asList("297e0896e4761529d979f40f5ad694db"));
Arrays.asList("02d134fd544613b1e5dd7f7197fc3753"));
executeTest("MAX 2 het sites [TEST THREE]; require PQ >= 30", spec);
}
@ -56,7 +56,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 5, 100)
+ " -L chr20:332341-382503",
1,
Arrays.asList("52a17f14692d726d3b726cf0ae7f2a09"));
Arrays.asList("2f7ec9904fc054c2ba1a7db05eb29334"));
executeTest("MAX 5 het sites [TEST FOUR]; require PQ >= 100", spec);
}
@ -66,7 +66,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 1000, 7, 10)
+ " -L chr20:332341-482503",
1,
Arrays.asList("af768f7958b8f4599c2374f1cc2fc613"));
Arrays.asList("da7a31725f229d1782dd3049848730aa"));
executeTest("MAX 7 het sites [TEST FIVE]; require PQ >= 10; cacheWindow = 1000", spec);
}
@ -76,7 +76,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
+ " -L chr20:652810-681757",
1,
Arrays.asList("3dd886672f59a47908b94136d0427bb0"));
Arrays.asList("e9d35cb88089fb0e8ae6678bfaeeac8c"));
executeTest("MAX 10 het sites [TEST SIX]; require PQ >= 10; cacheWindow = 20000; has inconsistent sites", spec);
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -27,7 +27,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf",
"d33212a84368e821cbedecd4f59756d6", // tranches
"4652dca41222bebdf9d9fda343b2a835", // recal file
"5350b1a4c1250cf3b77ca45327c04711"); // cut VCF
"243a397a33a935fcaccd5deb6d16f0c0"); // cut VCF
@DataProvider(name = "VRTest")
public Object[][] createData1() {

34
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -71,24 +71,24 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
}
@Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2117fff6e0d182cd20be508e9661829c", true); }
@Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2cfaf7af3dd119df08b8a9c1f72e2f93", " -setKey foo", true); }
@Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "1474ac0fde2ce42a3c24f1c97eab333e", " -setKey null", true); }
@Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "7fc66df048a0ab08cf507906e1d4a308", false); } // official project VCF files in tabix format
@Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "c608b9fc1e36dba6cebb4f259883f9f0", true); }
@Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "20caad94411d6ab48153b214de916df8", " -setKey foo", true); }
@Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "004f3065cb1bc2ce2f9afd695caf0b48", " -setKey null", true); }
@Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "c9c901ff9ef2a982624b203a8086dff0", false); } // official project VCF files in tabix format
@Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "ec9715f53dbf4531570557c212822f12", false); }
@Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "f1072be5f5c6ee810276d9ca6537224d", false); }
@Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "7593be578d4274d672fc22fced38012b", false); }
@Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "1cd467863c4e948fadd970681552d57e", false); }
@Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "b77a1eec725201d9d8e74ee0c45638d3", false); } // official project VCF files in tabix format
@Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "802977fdfd2f4905b501bb06800f60af", false); } // official project VCF files in tabix format
@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "a67157287dd2b24b5cdf7ebf8fcbbe9a", false); }
@Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "1d5a021387a8a86554db45a29f66140f", false); } // official project VCF files in tabix format
@Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "20163d60f18a46496f6da744ab5cc0f9", false); } // official project VCF files in tabix format
@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "5b82f37df1f5ba40f0474d71c94142ec", false); }
@Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e1f4718a179f1196538a33863da04f53", false); }
@Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "c58dca482bf97069eac6d9f1a07a2cba", false); }
@Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "b3783384b7c8e877b971033e90beba48", true); }
@Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "89f55abea8f59e39d1effb908440548c", true); }
@Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "902e541c87caa72134db6293fc46f0ad"); }
@Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "f339ad4bb5863b58b9c919ce7d040bb9"); }
@Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "4836086891f6cbdd40eebef3076d215a"); }
@Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "6a34b5d743efda8b2f3b639f3a2f5de8"); }
@Test public void threeWayWithRefs() {
WalkerTestSpec spec = new WalkerTestSpec(
@ -101,7 +101,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
" -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
" -genotypeMergeOptions UNIQUIFY -L 1"),
1,
Arrays.asList("a07995587b855f3214fb71940bf23c0f"));
Arrays.asList("8b78339ccf7a5a5a837f79e88a3a38e5"));
executeTest("threeWayWithRefs", spec);
}
@ -120,7 +120,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
}
// @Test public void complexTestFull() { combineComplexSites("", "64b991fd3850f83614518f7d71f0532f"); }
@Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "0db9ef50fe54b60426474273d7c7fa99"); }
@Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "d20acb3d53ba0a02ce92d540ebeda2a9"); }
@Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "8d1b3d120515f8b56b5a0d10bc5da713"); }
@Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "df96cb3beb2dbb5e02f80abec7d3571e"); }
@Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "f72a178137e25dbe0b931934cdc0079d"); }
@Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "f704caeaaaed6711943014b847fe381a"); }
}

6
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
View File

@ -40,7 +40,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LiftoverVariants -o %s -R " + b36KGReference + " -B:variant,vcf3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
1,
Arrays.asList("37e23efd7d6471fc0f807b31ccafe0eb"));
Arrays.asList("70aeaca5b74cc7ba8e2da7b71ff0fbfd"));
executeTest("test b36 to hg19", spec);
}
@ -49,7 +49,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LiftoverVariants -o %s -R " + b36KGReference + " -B:variant,vcf3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.unsortedSamples.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
1,
Arrays.asList("b6ef4a2f026fd3843aeb9ed764a66921"));
Arrays.asList("3fd7ec2dc4064ef410786276b0dc9d08"));
executeTest("test b36 to hg19, unsorted samples", spec);
}
@ -58,7 +58,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LiftoverVariants -o %s -R " + hg18Reference + " -B:variant,vcf " + validationDataLocation + "liftover_test.vcf -chain " + validationDataLocation + "hg18ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
1,
Arrays.asList("3275373b3c44ad14a270b50664b3f8a3"));
Arrays.asList("ab2c6254225d7e2ecf52eee604d5673b"));
executeTest("test hg18 to hg19, unsorted", spec);
}
}

8
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -18,7 +18,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' -B:variant,VCF3 " + testfile + " -NO_HEADER"),
1,
Arrays.asList("1b9d551298dc048c7d36b60440ff4d50")
Arrays.asList("d18516c1963802e92cb9e425c0b75fd6")
);
executeTest("testComplexSelection--" + testfile, spec);
@ -31,7 +31,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -sn A -sn B -sn C -B:variant,VCF3 " + testfile + " -NO_HEADER"),
1,
Arrays.asList("5ba7536a0819421b330350a160e4261a")
Arrays.asList("b74038779fe6485dbb8734ae48178356")
);
executeTest("testRepeatedLineSelection--" + testfile, spec);
@ -44,7 +44,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + hg19Reference + " -sn NA12878 -disc myvar -L 20:1012700-1020000 -B:variant,VCF " + b37hapmapGenotypes + " -B:myvar,VCF " + testFile + " -o %s -NO_HEADER",
1,
Arrays.asList("97621ae8f29955eedfc4e0be3515fcb9")
Arrays.asList("78e6842325f1f1bc9ab30d5e7737ee6e")
);
executeTest("testDiscordance--" + testFile, spec);
@ -57,7 +57,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + hg19Reference + " -sn NA12878 -conc hapmap -L 20:1012700-1020000 -B:hapmap,VCF " + b37hapmapGenotypes + " -B:variant,VCF " + testFile + " -o %s -NO_HEADER",
1,
Arrays.asList("a0ae016fdffcbe7bfb99fd3dbc311407")
Arrays.asList("d2ba3ea30a810f6f0fbfb1b643292b6a")
);
executeTest("testConcordance--" + testFile, spec);

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
View File

@ -60,7 +60,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
" --NO_HEADER" +
" -o %s",
1,
Arrays.asList("debbbf3e661b6857cc8d99ff7635bb1d")
Arrays.asList("658f580f7a294fd334bd897102616fed")
);
executeTest("testSimpleVCFStreaming", spec);

8
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
View File

@ -20,7 +20,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test
public void testVariantsToVCFUsingGeliInput() {
List<String> md5 = new ArrayList<String>();
md5.add("bd15d98adc76b5798e3bbeff3f936feb");
md5.add("815b82fff92aab41c209eedce2d7e7d9");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
@ -38,7 +38,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test
public void testGenotypesToVCFUsingGeliInput() {
List<String> md5 = new ArrayList<String>();
md5.add("acd15d3f85bff5b545bc353e0e23cc6e");
md5.add("22336ee9c12aa222ce29c3c5babca7d0");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
@ -56,7 +56,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test
public void testGenotypesToVCFUsingHapMapInput() {
List<String> md5 = new ArrayList<String>();
md5.add("6f34528569f8cf5941cb365fa77288c1");
md5.add("9bedaa7670b86a07be5191898c3727cf");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
@ -73,7 +73,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test
public void testGenotypesToVCFUsingVCFInput() {
List<String> md5 = new ArrayList<String>();
md5.add("d8316fc1b9d8e954a58940354119a32e");
md5.add("cc215edec9ca28e5c79ab1b67506f9f7");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +

2
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
View File

@ -49,7 +49,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -NO_HEADER -B:vcf,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s",
2, // just one output file
Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "e6673737acbb6bfabfcd92c4b2268241"));
Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "ff91731213fd0bbdc200ab6fd1c93e63"));
executeTest("testToVCF", spec);
}