diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java index 1f9e07382..3cd14e849 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java @@ -807,9 +807,9 @@ public class PhaseByTransmission extends RodWalker, HashMa updateTrioMetricsCounters(phasedMother,phasedFather,phasedChild,mvCount,metricsCounters); mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t%s:%s:%s:%s\t%s:%s:%s:%s\t%s:%s:%s:%s", vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(), - phasedMother.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getAttribute(VCFConstants.DEPTH_KEY),phasedMother.getAttribute("AD"),phasedMother.getLikelihoodsString(), - phasedFather.getGenotypeString(),phasedFather.getAttribute(VCFConstants.DEPTH_KEY),phasedFather.getAttribute(VCFConstants.GENOTYPE_ALLELE_DEPTHS),phasedFather.getLikelihoodsString(), - phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute(VCFConstants.GENOTYPE_ALLELE_DEPTHS),phasedChild.getLikelihoodsString()); + phasedMother.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getDP(),Arrays.asList(phasedMother.getAD()), + phasedMother.getLikelihoodsString(), phasedFather.getGenotypeString(),phasedFather.getDP(),Arrays.asList(phasedFather.getAD()),phasedFather.getLikelihoodsString(), + phasedChild.getGenotypeString(),Arrays.asList(phasedChild.getDP()),phasedChild.getAD(),phasedChild.getLikelihoodsString()); if(!(phasedMother.getType()==mother.getType() && phasedFather.getType()==father.getType() && phasedChild.getType()==child.getType())) metricsCounters.put(NUM_GENOTYPES_MODIFIED,metricsCounters.get(NUM_GENOTYPES_MODIFIED)+1); } @@ -819,8 +819,8 @@ public class PhaseByTransmission extends RodWalker, HashMa metricsCounters.put(NUM_GENOTYPES_MODIFIED,metricsCounters.get(NUM_GENOTYPES_MODIFIED)+1); mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t%s:%s:%s:%s\t.:.:.:.\t%s:%s:%s:%s", vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(), - phasedMother.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getAttribute(VCFConstants.DEPTH_KEY),phasedMother.getAttribute(VCFConstants.GENOTYPE_ALLELE_DEPTHS),phasedMother.getLikelihoodsString(), - phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute(VCFConstants.GENOTYPE_ALLELE_DEPTHS),phasedChild.getLikelihoodsString()); + phasedMother.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getDP(),Arrays.asList(phasedMother.getAD()),phasedMother.getLikelihoodsString(), + phasedChild.getGenotypeString(),phasedChild.getDP(),Arrays.asList(phasedChild.getAD()),phasedChild.getLikelihoodsString()); } } else{ @@ -830,8 +830,8 @@ public class PhaseByTransmission extends RodWalker, HashMa metricsCounters.put(NUM_GENOTYPES_MODIFIED,metricsCounters.get(NUM_GENOTYPES_MODIFIED)+1); mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t.:.:.:.\t%s:%s:%s:%s\t%s:%s:%s:%s", vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(), - phasedFather.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedFather.getGenotypeString(),phasedFather.getAttribute(VCFConstants.DEPTH_KEY),phasedFather.getAttribute(VCFConstants.GENOTYPE_ALLELE_DEPTHS),phasedFather.getLikelihoodsString(), - phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute(VCFConstants.GENOTYPE_ALLELE_DEPTHS),phasedChild.getLikelihoodsString()); + phasedFather.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedFather.getGenotypeString(),phasedFather.getDP(),Arrays.asList(phasedFather.getAD()),phasedFather.getLikelihoodsString(), + phasedChild.getGenotypeString(),phasedChild.getDP(),Arrays.asList(phasedChild.getAD()),phasedChild.getLikelihoodsString()); } //Report violation if set so diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java index cb19df13e..014381bea 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java @@ -241,7 +241,7 @@ public class VariantSummary extends VariantEvaluator implements StandardEval { // update transition / transversion ratio if ( titvTable != null ) titvTable.inc(type, g.getSampleName()); - if ( g.hasAttribute(VCFConstants.DEPTH_KEY) ) + if ( g.hasDP() ) depthPerSample.inc(type, g.getSampleName()); } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index b0f4c569a..3e84e9c52 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -401,6 +401,7 @@ public class SelectVariants extends RodWalker implements TreeR Collection XLsamplesFromFile = SampleUtils.getSamplesFromFiles(XLsampleFiles); samples.removeAll(XLsamplesFromFile); samples.removeAll(XLsampleNames); + NO_SAMPLES_SPECIFIED = NO_SAMPLES_SPECIFIED && XLsampleNames.isEmpty(); if ( samples.size() == 0 && !NO_SAMPLES_SPECIFIED ) throw new UserException("All samples requested to be included were also requested to be excluded."); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java index aaf3bb5cd..1ffb78124 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java @@ -288,8 +288,8 @@ public class VariantsToBinaryPed extends RodWalker { private byte getStandardEncoding(Genotype g, int offset) { byte b; - if ( g.hasAttribute(VCFConstants.GENOTYPE_QUALITY_KEY) && ((Integer) g.getAttribute(VCFConstants.GENOTYPE_QUALITY_KEY)) < minGenotypeQuality ) { - b = NO_CALL; + if ( g.hasGQ() && g.getGQ() < minGenotypeQuality ) { + b = NO_CALL; } else if ( g.isHomRef() ) { b = HOM_REF; } else if ( g.isHomVar() ) { @@ -305,7 +305,7 @@ public class VariantsToBinaryPed extends RodWalker { private byte getFlippedEncoding(Genotype g, int offset) { byte b; - if ( g.hasAttribute(VCFConstants.GENOTYPE_QUALITY_KEY) && ((Integer) g.getAttribute(VCFConstants.GENOTYPE_QUALITY_KEY)) < minGenotypeQuality ) { + if ( g.hasGQ() && g.getGQ() < minGenotypeQuality ) { b = NO_CALL; } else if ( g.isHomRef() ) { b = HOM_VAR; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index 02485108c..5d86a0c5e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -26,6 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.variantcontext.Allele; @@ -314,8 +315,12 @@ public class VariantsToTable extends RodWalker { if ( addGenotypeFields ) { for ( final String sample : samples ) { for ( final String gf : genotypeFields ) { - if ( vc.hasGenotype(sample) && vc.getGenotype(sample).hasAttribute(gf) ) - addFieldValue(vc.getGenotype(sample).getAttribute(gf), records); + if ( vc.hasGenotype(sample) && vc.getGenotype(sample).hasAnyAttribute(gf) ) { + if ( gf.equals(VCFConstants.GENOTYPE_KEY) ) + addFieldValue(vc.getGenotype(sample).getGenotypeString(true), records); + else + addFieldValue(vc.getGenotype(sample).getAnyAttribute(gf), records); + } else addFieldValue(MISSING_DATA, records); } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java index 026b2ea15..3db380489 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java @@ -782,6 +782,8 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec gb.AD(decodeInts(GTValueArray[i])); } else if (gtKey.equals(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY)) { gb.PL(decodeInts(GTValueArray[i])); + } else if (gtKey.equals(VCFConstants.GENOTYPE_LIKELIHOODS_KEY)) { + gb.PL(GenotypeLikelihoods.fromGLField(GTValueArray[i]).getAsPLs()); } else if (gtKey.equals(VCFConstants.DEPTH_KEY)) { gb.DP(Integer.valueOf(GTValueArray[i])); } else { diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java index 0affcc070..c1cd0068e 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java @@ -336,7 +336,7 @@ public class Allele implements Comparable { * * @return the segregating bases */ - public String getBaseString() { return new String(getBases()); } + public String getBaseString() { return isNoCall() ? NO_CALL_STRING : new String(getBases()); } /** * Return the printed representation of this allele. diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java index 75b893757..6df6d5f70 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java @@ -325,7 +325,7 @@ public abstract class Genotype implements Comparable { @Ensures("result != null || ! isAvailable()") public String getGenotypeString(boolean ignoreRefState) { if ( getPloidy() == 0 ) - return null; + return "NA"; // Notes: // 1. Make sure to use the appropriate separator depending on whether the genotype is phased @@ -419,7 +419,7 @@ public abstract class Genotype implements Comparable { * @param key a non-null string key to check for an association * @return true if key has a value in the extendedAttributes */ - @Requires("key != null") + @Requires({"key != null", "! isForbiddenKey(key)"}) public boolean hasAttribute(final String key) { return getExtendedAttributes().containsKey(key); } @@ -431,7 +431,7 @@ public abstract class Genotype implements Comparable { * @param defaultValue the value to return if key isn't in the extended attributes * @return a value (potentially) null associated with key, or defaultValue if no association exists */ - @Requires("key != null") + @Requires({"key != null", "! isForbiddenKey(key)"}) @Ensures("hasAttribute(key) || result == defaultValue") public Object getAttribute(final String key, final Object defaultValue) { return hasAttribute(key) ? getExtendedAttributes().get(key) : defaultValue; @@ -490,6 +490,46 @@ public abstract class Genotype implements Comparable { return Double.valueOf((String)x); // throws an exception if this isn't a string } + /** + * A totally generic getter, that allows you to specific keys that correspond + * to even inline values (GQ, for example). Can be very expensive. Additionally, + * all int[] are converted inline into List for convenience. + * + * @param key + * @return + */ + public Object getAnyAttribute(final String key) { + if (key.equals(VCFConstants.GENOTYPE_KEY)) { + return getAlleles(); + } else if (key.equals(VCFConstants.GENOTYPE_QUALITY_KEY)) { + return getGQ(); + } else if (key.equals(VCFConstants.GENOTYPE_ALLELE_DEPTHS)) { + return Arrays.asList(getAD()); + } else if (key.equals(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY)) { + return Arrays.asList(getPL()); + } else if (key.equals(VCFConstants.DEPTH_KEY)) { + return getDP(); + } else { + return getAttribute(key); + } + } + + public boolean hasAnyAttribute(final String key) { + if (key.equals(VCFConstants.GENOTYPE_KEY)) { + return isAvailable(); + } else if (key.equals(VCFConstants.GENOTYPE_QUALITY_KEY)) { + return hasGQ(); + } else if (key.equals(VCFConstants.GENOTYPE_ALLELE_DEPTHS)) { + return hasAD(); + } else if (key.equals(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY)) { + return hasPL(); + } else if (key.equals(VCFConstants.DEPTH_KEY)) { + return hasDP(); + } else { + return hasAttribute(key); + } + } + // TODO -- add getAttributesAsX interface here // ------------------------------------------------------------------------------ @@ -567,4 +607,8 @@ public abstract class Genotype implements Comparable { return true; return false; } + + protected final static boolean isForbiddenKey(final String key) { + return PRIMARY_KEYS.contains(key); + } } \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/SlowGenotype.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/SlowGenotype.java index 3cca86b30..6f7dda2bd 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/SlowGenotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/SlowGenotype.java @@ -72,8 +72,8 @@ public class SlowGenotype extends Genotype { // Useful methods for getting genotype likelihoods for a genotype object, if present // @Override public boolean hasLikelihoods() { - return (hasAttribute(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY) && !getAttribute(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY).equals(VCFConstants.MISSING_VALUE_v4)) || - (hasAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY) && !getAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY).equals(VCFConstants.MISSING_VALUE_v4)); + return (commonInfo.hasAttribute(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY) && !commonInfo.getAttribute(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY).equals(VCFConstants.MISSING_VALUE_v4)) || + (commonInfo.hasAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY) && !commonInfo.getAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY).equals(VCFConstants.MISSING_VALUE_v4)); } @Override public GenotypeLikelihoods getLikelihoods() { @@ -87,7 +87,7 @@ public class SlowGenotype extends Genotype { } private GenotypeLikelihoods getLikelihoods(String key, boolean asPL) { - Object x = getAttribute(key); + Object x = commonInfo.getAttribute(key); if ( x instanceof String ) { if ( asPL ) return GenotypeLikelihoods.fromPLField((String)x); @@ -145,25 +145,25 @@ public class SlowGenotype extends Genotype { @Override public int getDP() { - return getAttributeAsInt(VCFConstants.DEPTH_KEY, -1); + return commonInfo.getAttributeAsInt(VCFConstants.DEPTH_KEY, -1); } @Override public boolean hasDP() { - return hasAttribute(VCFConstants.DEPTH_KEY); + return commonInfo.hasAttribute(VCFConstants.DEPTH_KEY); } @Override public int[] getAD() { if ( hasAD() ) { - return (int[])getAttribute(VCFConstants.GENOTYPE_ALLELE_DEPTHS); + return (int[])commonInfo.getAttribute(VCFConstants.GENOTYPE_ALLELE_DEPTHS); } else return null; } @Override public boolean hasAD() { - return hasAttribute(VCFConstants.GENOTYPE_ALLELE_DEPTHS); + return commonInfo.hasAttribute(VCFConstants.GENOTYPE_ALLELE_DEPTHS); } @Override diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java index 13752e36f..6ecb898df 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java @@ -192,7 +192,7 @@ class JEXLMap implements Map { infoMap.put("isHomRef", g.isHomRef() ? "1" : "0"); infoMap.put("isHet", g.isHet() ? "1" : "0"); infoMap.put("isHomVar", g.isHomVar() ? "1" : "0"); - infoMap.put(VCFConstants.GENOTYPE_QUALITY_KEY, g.getPhredScaledQual()); + infoMap.put(VCFConstants.GENOTYPE_QUALITY_KEY, g.getGQ()); for ( Map.Entry e : g.getExtendedAttributes().entrySet() ) { if ( e.getValue() != null && !e.getValue().equals(VCFConstants.MISSING_VALUE_v4) ) infoMap.put(e.getKey(), e.getValue()); diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java index 2574753bd..68de0656f 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java @@ -329,6 +329,8 @@ class VCFWriter extends IndexingVariantContextWriter { */ private void addGenotypeData(VariantContext vc, Map alleleMap, List genotypeFormatKeys) throws IOException { + if ( mHeader.getGenotypeSamples().size() != vc.getNSamples() ) + throw new ReviewedStingException("BUG: number of VariantContext samples " + vc.getNSamples() + " != to the number of sample found in the VCF header" + mHeader.getGenotypeSamples().size()); for ( String sample : mHeader.getGenotypeSamples() ) { mWriter.write(VCFConstants.FIELD_SEPARATOR); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java index 4a1af4e92..cb541c895 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java @@ -47,7 +47,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest { @Test public void testb36Tohg19UnsortedSamples() { WalkerTestSpec spec = new WalkerTestSpec( - "-T LiftoverVariants -o %s -R " + b36KGReference + " --variant " + testDir + "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", + "-T LiftoverVariants -o %s -R " + b36KGReference + " --variant " + 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("07d1bf52125d1f9a25e260e13ec7b010")); executeTest("test b36 to hg19, unsorted samples", spec); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java index bbfbf9c1e..61da953d8 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java @@ -56,7 +56,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants" + " -R " + b36KGReference + - " --variant,storage=STREAM " + tmpFifo.getAbsolutePath() + + " --variant:VCF,storage=STREAM " + tmpFifo.getAbsolutePath() + " --no_cmdline_in_header " + " -o %s", 1, @@ -80,7 +80,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest { WalkerTestSpec selectTestSpec = new WalkerTestSpec( "-T SelectVariants" + " -R " + b36KGReference + - " --variant,storage=STREAM " + testFile + + " --variant:VCF,storage=STREAM " + testFile + " --no_cmdline_in_header" + " -select 'QD > 2.0'" + " -o " + tmpFifo.getAbsolutePath(), diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java index 85773aa27..e3c74b5aa 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java @@ -87,6 +87,19 @@ public class VariantsToTableIntegrationTest extends WalkerTest { executeTest("testGenotypeFields", spec); } + @Test(enabled = true) + public void testGenotypeFieldsWithInline() { + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( + "-R " + b36KGReference + + " --variant " + testDir + "vcfexample2.vcf" + + " -T VariantsToTable" + + " -GF RD -GF GT -GF GQ" + + " -o %s", + 1, + Arrays.asList("29744059742ae71fd6aabd29e5c391fb")); + executeTest("testGenotypeFieldsWithInline", spec); + } + @Test(enabled = true) public void testMoltenOutput() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(