From 4fc1db7aaf98556e92fa053d4eed5616645bfa59 Mon Sep 17 00:00:00 2001 From: delangel Date: Fri, 23 Jul 2010 20:24:03 +0000 Subject: [PATCH] Change interface to VCFWriter add() method to take only 1 byte from reference (since that's the only thing it needs), to prevent bugs like having people call it with ref.addBases() which is wrong (since it provides bases starting from the left of reference context window). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3868 348d0f76-0448-11de-a6fe-93d51630548a --- .../variantcontext/VariantContextUtils.java | 18 +++++++++--------- .../sting/gatk/walkers/VariantsToVCF.java | 2 +- .../walkers/annotator/VariantAnnotator.java | 4 ++-- .../filters/VariantFiltrationWalker.java | 2 +- .../walkers/genotyper/BatchedCallsMerger.java | 2 +- .../sequenom/SequenomValidationConverter.java | 2 +- .../walkers/varianteval/VariantEvalWalker.java | 2 +- .../variantrecalibration/ApplyVariantCuts.java | 2 +- .../VariantRecalibrator.java | 4 ++-- .../walkers/variantutils/CombineVariants.java | 4 ++-- .../variantutils/FilterLiftedVariants.java | 2 +- .../walkers/variantutils/LiftoverVariants.java | 2 +- .../oneoffprojects/walkers/IndelAnnotator.java | 2 +- .../walkers/IndelDBRateWalker.java | 6 +++--- .../walkers/MendelianViolationClassifier.java | 2 +- .../walkers/TestVariantContextWalker.java | 2 +- .../walkers/VCF4WriterTestWalker.java | 2 +- .../gatk/walkers/BeagleOutputToVCFWalker.java | 2 +- .../gatk/walkers/TrioGenotyperWalker.java | 2 +- .../walkers/annotator/GenomicAnnotator.java | 4 ++-- .../gatk/walkers/vcftools/VariantSelect.java | 2 +- .../gatk/walkers/vcftools/VariantSubset.java | 2 +- .../genotype/vcf/VCFGenotypeWriterAdapter.java | 4 ++-- .../sting/utils/genotype/vcf/VCFWriter.java | 6 ++---- .../utils/genotype/vcf/VCFWriterUnitTest.java | 4 ++-- 25 files changed, 42 insertions(+), 44 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java index 4a20e2951..4ab7d466d 100755 --- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java +++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java @@ -171,8 +171,8 @@ public class VariantContextUtils { UNION, INTERSECT } - public static VariantContext simpleMerge(Collection unsortedVCs, byte[] refBases) { - return simpleMerge(unsortedVCs, null, VariantMergeType.INTERSECT, GenotypeMergeType.UNSORTED, false, false, refBases); + public static VariantContext simpleMerge(Collection unsortedVCs, byte refBase) { + return simpleMerge(unsortedVCs, null, VariantMergeType.INTERSECT, GenotypeMergeType.UNSORTED, false, false, refBase); } @@ -189,14 +189,14 @@ public class VariantContextUtils { */ public static VariantContext simpleMerge(Collection unsortedVCs, List priorityListOfVCs, VariantMergeType variantMergeOptions, GenotypeMergeType genotypeMergeOptions, - boolean annotateOrigin, boolean printMessages, byte[] inputRefBases ) { + boolean annotateOrigin, boolean printMessages, byte inputRefBase ) { - return simpleMerge(unsortedVCs, priorityListOfVCs, variantMergeOptions, genotypeMergeOptions, annotateOrigin, printMessages, inputRefBases, "set"); + return simpleMerge(unsortedVCs, priorityListOfVCs, variantMergeOptions, genotypeMergeOptions, annotateOrigin, printMessages, inputRefBase, "set"); } public static VariantContext simpleMerge(Collection unsortedVCs, List priorityListOfVCs, VariantMergeType variantMergeOptions, GenotypeMergeType genotypeMergeOptions, - boolean annotateOrigin, boolean printMessages, byte[] inputRefBases, String setKey ) { + boolean annotateOrigin, boolean printMessages, byte inputRefBase, String setKey ) { if ( unsortedVCs == null || unsortedVCs.size() == 0 ) return null; @@ -213,7 +213,7 @@ public static VariantContext simpleMerge(Collection unsortedVCs, List VCs = new ArrayList(); for (VariantContext vc : prepaddedVCs) { - VCs.add(createVariantContextWithPaddedAlleles(vc,inputRefBases)); + VCs.add(createVariantContextWithPaddedAlleles(vc,inputRefBase)); } @@ -479,7 +479,7 @@ public static VariantContext simpleMerge(Collection unsortedVCs, } - public static VariantContext createVariantContextWithPaddedAlleles(VariantContext inputVC, byte[] inputRefBase) { + public static VariantContext createVariantContextWithPaddedAlleles(VariantContext inputVC, byte inputRefBase) { Allele refAllele = inputVC.getReference(); @@ -501,8 +501,8 @@ public static VariantContext simpleMerge(Collection unsortedVCs, Map attributes = inputVC.getAttributes(); - if (BaseUtils.isRegularBase(inputRefBase[0])) - refByte = inputRefBase[0]; + if (BaseUtils.isRegularBase(inputRefBase)) + refByte = inputRefBase; else if (attributes.containsKey(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY)) refByte = (Byte)attributes.get(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY); else diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java b/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java index 8c7b8279f..7d34eeae7 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java @@ -129,7 +129,7 @@ public class VariantsToVCF extends RodWalker { } vc = VariantContextUtils.purgeUnallowedGenotypeAttributes(vc, allowedGenotypeFormatStrings); - vcfwriter.add(vc, new byte[]{ref}); + vcfwriter.add(vc,ref); } public Integer reduceInit() { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index aca29d7e7..ca696e664 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -202,12 +202,12 @@ public class VariantAnnotator extends RodWalker { if ( ! indelsOnly ) { for ( VariantContext annotatedVC : annotatedVCs ) - vcfWriter.add(annotatedVC, new byte[]{ref.getBase()}); + vcfWriter.add(annotatedVC, ref.getBase()); } else { // check to see if the buffered context is different (in location) this context if ( indelBufferContext != null && ! indelBufferContext.iterator().next().getLocation().equals(annotatedVCs.iterator().next().getLocation()) ) { for ( VariantContext annotatedVC : indelBufferContext ) - vcfWriter.add(annotatedVC, new byte[]{ref.getBase()}); + vcfWriter.add(annotatedVC, ref.getBase()); indelBufferContext = annotatedVCs; } else { indelBufferContext = annotatedVCs; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java index cc36e44c3..6a6678ee7 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java @@ -216,7 +216,7 @@ public class VariantFiltrationWalker extends RodWalker { private void writeVCF(VariantContext vc, byte ref) { if ( writer == null ) initializeVcfWriter(vc); - writer.add(vc, new byte[]{ref}); + writer.add(vc, ref); } public Integer reduce(Integer value, Integer sum) { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java index a72ed4552..3f65c0677 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java @@ -148,7 +148,7 @@ public class BatchedCallsMerger extends LocusWalker imp } // merge the variant contexts - return VariantContextUtils.simpleMerge(calls, ref.getBases()); + return VariantContextUtils.simpleMerge(calls, ref.getBase()); } private AlignmentContext filterForSamples(ReadBackedPileup pileup, Set samples) { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java index e075a695c..db0759b4b 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java @@ -160,7 +160,7 @@ public class SequenomValidationConverter extends RodWalker record : records ) - vcfWriter.add(record.first, new byte[]{record.second}); + vcfWriter.add(record.first, record.second); vcfWriter.close(); } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index 83732cfb6..4b69e4be2 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -554,7 +554,7 @@ public class VariantEvalWalker extends RodWalker { wroteHeader = true; } - writer.add(mvc, new byte[]{ref}); + writer.add(mvc, ref); //interestingReasons.clear(); } } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java index 52035108d..b8a875777 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java @@ -150,7 +150,7 @@ public class ApplyVariantCuts extends RodWalker { vc = new VariantContext(vc.getName(), vc.getLocation(), vc.getAlleles(), vc.getGenotypes(), vc.getNegLog10PError(), filters, vc.getAttributes()); } } - vcfWriter.add( vc, new byte[]{ref.getBase()} ); + vcfWriter.add( vc, ref.getBase() ); } } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java index d3c3e6b60..eb72f6db7 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java @@ -194,10 +194,10 @@ public class VariantRecalibrator extends RodWalker { // Need to provide reference bases to simpleMerge starting at current locus Collection vcs = tracker.getAllVariantContexts(ref, context.getLocation()); VariantContext mergedVC = VariantContextUtils.simpleMerge(vcs, priority, variantMergeOption, - genotypeMergeOption, true, printComplexMerges, ref.getBasesAtLocus(1), SET_KEY); + genotypeMergeOption, true, printComplexMerges, ref.getBase(), SET_KEY); //out.printf(" merged => %s%nannotated => %s%n", mergedVC, annotatedMergedVC); if ( mergedVC != null ) { // only operate at the start of events VariantContext annotatedMergedVC = engine.annotateContext(tracker, ref, mergedVC); - vcfWriter.add(annotatedMergedVC, ref.getBasesAtLocus(1)); + vcfWriter.add(annotatedMergedVC, ref.getBase()); } return vcs.isEmpty() ? 0 : 1; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java index 5a6d2c231..be8f62654 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java @@ -64,7 +64,7 @@ public class FilterLiftedVariants extends RodWalker { if ( recordRef != ref ) { failedLocs++; } else { - writer.add(vc, new byte[]{ref}); + writer.add(vc, ref); } } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java index cf2828eea..4010d70bf 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java @@ -86,7 +86,7 @@ public class LiftoverVariants extends RodWalker { if ( toInterval != null ) { vc = VariantContextUtils.modifyLocation(vc, GenomeLocParser.createGenomeLoc(toInterval.getSequence(), toInterval.getStart(), toInterval.getEnd())); - writer.add(vc, new byte[]{ref.getBase()}); + writer.add(vc, ref.getBase()); successfulIntervals++; } else { failedIntervals++; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java index b561cfdb0..eaa42b354 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java @@ -109,7 +109,7 @@ public class IndelAnnotator extends RodWalker{ Map attrs = new HashMap(vc.getAttributes()); attrs.put("type",annotationString); vc = VariantContextUtils.modifyAttributes(vc, attrs); - vcfWriter.add(vc, new byte[]{ref.getBase()}); + vcfWriter.add(vc, ref.getBase()); return 1; } diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java index 4a9b2d5b6..3acbf3538 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java @@ -142,12 +142,12 @@ public class IndelDBRateWalker extends RodWalker if ( vcfWriter != null ) { int i = 0; while ( i < compContexts.size() && compContexts.get(i).getLocation().isBefore(evalContexts.get(0).getLocation())) { - vcfWriter.add(compContexts.get(i), new byte[]{compContexts.get(i).getReference().getBases()[0]}); + vcfWriter.add(compContexts.get(i),compContexts.get(i).getReference().getBases()[0]); i++; } - vcfWriter.add(evalContexts.get(0), new byte[]{ref.getBase()}); + vcfWriter.add(evalContexts.get(0), ref.getBase()); while ( i < compContexts.size() && compContexts.get(i).getLocation().distance(evalContexts.get(0).getLocation()) <= indelWindow) { - vcfWriter.add(compContexts.get(i), new byte[]{compContexts.get(i).getReference().getBases()[0]}); + vcfWriter.add(compContexts.get(i), compContexts.get(i).getReference().getBases()[0]); i++; } } diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java index 097cd5847..9a699839f 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java @@ -601,7 +601,7 @@ public class MendelianViolationClassifier extends LocusWalker { wroteHeader = true; } - writer.add(vc, new byte[]{ref.getBase()}); + writer.add(vc, ref.getBase()); } n++; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java index 5834309dc..46c5ff0cb 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java @@ -126,7 +126,7 @@ public class VCF4WriterTestWalker extends RodWalker { return 0; // Write directly variant context to VCF4.0 format. - vcfWriter.add(vc, ref.getBases()); + vcfWriter.add(vc, ref.getBase()); return 1; } diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java index 35f7e9940..1ecc313f0 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java @@ -317,7 +317,7 @@ public class BeagleOutputToVCFWalker extends RodWalker { - vcfWriter.add(VariantContextUtils.modifyAttributes(filteredVC, attributes), new byte[]{ref.getBase()}); + vcfWriter.add(VariantContextUtils.modifyAttributes(filteredVC, attributes), ref.getBase()); return 1; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java index 6a0759ac8..59d514d5d 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java @@ -179,7 +179,7 @@ public class TrioGenotyperWalker extends RefWalker{ if ( a == 0 ) writer.writeHeader(VariantContextAdaptors.createVCFHeader(null, vc)); - writer.add(vc, new byte[]{(byte)'.'}); + writer.add(vc, (byte)'.'); a++; } diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java index 8e56133f0..07c57a585 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java @@ -303,7 +303,7 @@ public class GenomicAnnotator extends RodWalker, Link } else { //write results to disk immediately for(VariantContext annotatedVC : annotatedVCs ) { - vcfWriter.add(annotatedVC, new byte[]{ref.getBase()}); + vcfWriter.add(annotatedVC,ref.getBase()); } } @@ -346,7 +346,7 @@ public class GenomicAnnotator extends RodWalker, Link if(multiThreadedMode) { //finally write results to disk for(VariantContext vc : totalOutputRecords ) { - vcfWriter.add(vc, vc.getReference().getBases()); + vcfWriter.add(vc, vc.getReference().getBases()[0]); } } diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSelect.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSelect.java index 2ddbeff48..e772e7208 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSelect.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSelect.java @@ -139,7 +139,7 @@ public class VariantSelect extends RodWalker { } if ( someoneMatched ) - writer.add(vc, new byte[]{ref.getBase()}); + writer.add(vc, ref.getBase()); return 1; } diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSubset.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSubset.java index edf4c0b0c..df901557f 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSubset.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSubset.java @@ -73,7 +73,7 @@ public class VariantSubset extends RodWalker { if ( (vc.isPolymorphic() || INCLUDE_NON_VARIANTS) && (!subset.isFiltered() || INCLUDE_FILTERED) ) - writer.add(subset, new byte[]{ref.getBase()}); + writer.add(subset, ref.getBase()); } return 1; diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java index 91008f7af..3dd6feffb 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java @@ -63,7 +63,7 @@ public class VCFGenotypeWriterAdapter extends VCFWriter implements VCFGenotypeWr public void addCall(VariantContext vc, byte ref) { vc = VariantContextUtils.purgeUnallowedGenotypeAttributes(vc, allowedGenotypeFormatKeys); - add(vc, new byte[]{ref}); + add(vc, ref); } public void writeHeader(VCFHeader header) { @@ -112,7 +112,7 @@ public class VCFGenotypeWriterAdapter extends VCFWriter implements VCFGenotypeWr while ( iterator.hasNext() ) { VariantContext vc = iterator.next(); vc = VariantContextUtils.purgeUnallowedGenotypeAttributes(vc, allowedGenotypeFormatKeys); - add(vc, new byte[]{vc.getReferenceBaseForIndel()}); + add(vc, vc.getReferenceBaseForIndel()); } vcfReader.close(); } catch (FileNotFoundException e) { diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java index 0aac8bc2f..ef354735b 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java @@ -133,15 +133,13 @@ public class VCFWriter { } } - public void add(VariantContext vc, byte[] refBases) { + public void add(VariantContext vc, byte refBase) { if ( mHeader == null ) throw new IllegalStateException("The VCF Header must be written before records can be added"); - if ( refBases == null || refBases.length < 1 ) - throw new IllegalArgumentException("The reference base must be provided to write VCF records"); try { - vc = VariantContextUtils.createVariantContextWithPaddedAlleles(vc, refBases); + vc = VariantContextUtils.createVariantContextWithPaddedAlleles(vc, refBase); GenomeLoc loc = vc.getLocation(); Map alleleMap = new HashMap(vc.getAlleles().size()); diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java index 1cbea1029..d209740b4 100644 --- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java @@ -47,8 +47,8 @@ public class VCFWriterUnitTest extends BaseTest { VCFHeader header = createFakeHeader(metaData,additionalColumns); VCFWriter writer = new VCFWriter(fakeVCFFile); writer.writeHeader(header); - writer.add(createVC(header),"A".getBytes()); - writer.add(createVC(header),"A".getBytes()); + writer.add(createVC(header),new Byte("A")); + writer.add(createVC(header),new Byte("A")); writer.close(); VCFCodec reader = new VCFCodec(); AsciiLineReader lineReader;