Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
This commit is contained in:
Guillermo del Angel
commit
c504a42137
|
|
@ -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);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -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);
|
||||
}
|
||||
|
|
@ -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")); }
|
||||
}
|
||||
|
|
@ -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) {
|
||||
|
|
|
|||
|
|
@ -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());
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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)")); }
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
}
|
||||
}
|
||||
|
|
@ -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;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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;
|
||||
|
|
|
|||
|
|
@ -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> {
|
||||
|
|
|
|||
|
|
@ -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> {
|
||||
|
|
|
|||
|
|
@ -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!
|
||||
|
|
|
|||
|
|
@ -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) ?
|
||||
|
|
|
|||
|
|
@ -867,7 +867,10 @@ public class VariantContext implements Feature { // to enable tribble intergrati
|
|||
|
||||
for ( String name : sampleNames ) {
|
||||
if ( map.containsKey(name) ) throw new IllegalArgumentException("Duplicate names detected in requested samples " + sampleNames);
|
||||
map.put(name, getGenotype(name));
|
||||
final Genotype g = getGenotype(name);
|
||||
if ( g != null ) {
|
||||
map.put(name, g);
|
||||
}
|
||||
}
|
||||
|
||||
return map;
|
||||
|
|
|
|||
|
|
@ -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,
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -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() {
|
||||
|
|
|
|||
|
|
@ -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"); }
|
||||
}
|
||||
|
|
@ -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);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
|
|
|
|||
|
|
@ -60,7 +60,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
|
|||
" --NO_HEADER" +
|
||||
" -o %s",
|
||||
1,
|
||||
Arrays.asList("debbbf3e661b6857cc8d99ff7635bb1d")
|
||||
Arrays.asList("658f580f7a294fd334bd897102616fed")
|
||||
);
|
||||
|
||||
executeTest("testSimpleVCFStreaming", spec);
|
||||
|
|
|
|||
|
|
@ -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 +
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue