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

java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java

@@ -171,8 +171,8 @@ public class VariantContextUtils {
         UNION, INTERSECT
     }
 
-    public static VariantContext simpleMerge(Collection<VariantContext> unsortedVCs, byte[] refBases) {
+    public static VariantContext simpleMerge(Collection<VariantContext> unsortedVCs, byte refBase) {
-        return simpleMerge(unsortedVCs, null, VariantMergeType.INTERSECT, GenotypeMergeType.UNSORTED, false, false, refBases);
+        return simpleMerge(unsortedVCs, null, VariantMergeType.INTERSECT, GenotypeMergeType.UNSORTED, false, false, refBase);
     }
 
 
@@ -189,14 +189,14 @@ public class VariantContextUtils {
      */
     public static VariantContext simpleMerge(Collection<VariantContext> unsortedVCs, List<String> 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<VariantContext> unsortedVCs, List<String> 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<VariantContext> unsortedVCs,
         List<VariantContext> VCs = new ArrayList<VariantContext>();
 
         for (VariantContext vc : prepaddedVCs) {
-            VCs.add(createVariantContextWithPaddedAlleles(vc,inputRefBases));
+            VCs.add(createVariantContextWithPaddedAlleles(vc,inputRefBase));
         }
 
 
@@ -479,7 +479,7 @@ public static VariantContext simpleMerge(Collection<VariantContext> 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<VariantContext> unsortedVCs,
 
             Map<String,Object> attributes = inputVC.getAttributes();
 
-            if (BaseUtils.isRegularBase(inputRefBase[0]))
+            if (BaseUtils.isRegularBase(inputRefBase))
-                refByte = inputRefBase[0];
+                refByte = inputRefBase;
             else if (attributes.containsKey(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY))
                 refByte = (Byte)attributes.get(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY);
             else

java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java

@@ -129,7 +129,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
         }
 
         vc = VariantContextUtils.purgeUnallowedGenotypeAttributes(vc, allowedGenotypeFormatStrings);
-        vcfwriter.add(vc, new byte[]{ref});
+        vcfwriter.add(vc,ref);
     }
 
     public Integer reduceInit() {

java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java

@@ -202,12 +202,12 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
 
         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;

java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java

@@ -216,7 +216,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
     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) {

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java

@@ -148,7 +148,7 @@ public class BatchedCallsMerger extends LocusWalker<VariantContext, Integer> imp
         }
 
         // merge the variant contexts
-        return VariantContextUtils.simpleMerge(calls, ref.getBases());
+        return VariantContextUtils.simpleMerge(calls, ref.getBase());
     }
 
     private AlignmentContext filterForSamples(ReadBackedPileup pileup, Set<String> samples) {

java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java

@@ -160,7 +160,7 @@ public class SequenomValidationConverter extends RodWalker<Pair<VariantContext,
         vcfWriter.writeHeader(header);
 
         for ( Pair<VariantContext, Byte> record : records )
-            vcfWriter.add(record.first, new byte[]{record.second});
+            vcfWriter.add(record.first, record.second);
         vcfWriter.close();
     }
 

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java

@@ -554,7 +554,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
                 wroteHeader = true;
             }
 
-            writer.add(mvc, new byte[]{ref});
+            writer.add(mvc, ref);
             //interestingReasons.clear();
         }
     }

java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java

@@ -150,7 +150,7 @@ public class ApplyVariantCuts extends RodWalker<Integer, Integer> {
                         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() );
             }
 
         }

java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java

@@ -194,10 +194,10 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
                     filters.add(VCFConstants.PASSES_FILTERS_v4);
                     VariantContext newVC = new VariantContext(vc.getName(), vc.getLocation(), vc.getAlleles(), vc.getGenotypes(), variantDatum.qual / 10.0, filters, attrs);
 
-                    vcfWriter.add( newVC, new byte[]{ref.getBase()} );
+                    vcfWriter.add( newVC, ref.getBase() );
 
                 } else { // not a SNP or is filtered so just dump it out to the VCF file
-                    vcfWriter.add( vc, new byte[]{ref.getBase()} ); 
+                    vcfWriter.add( vc, ref.getBase() ); 
                 }
             }
 

java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java

@@ -116,14 +116,14 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
         // Need to provide reference bases to simpleMerge starting at current locus
         Collection<VariantContext> 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;

java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java

@@ -64,7 +64,7 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
         if ( recordRef != ref ) {
             failedLocs++;
         } else {
-            writer.add(vc, new byte[]{ref});
+            writer.add(vc, ref);
         }
     }
 

java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java

@@ -86,7 +86,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
 
         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++;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java

@@ -109,7 +109,7 @@ public class IndelAnnotator extends RodWalker<Integer,Long>{
         Map<String, Object> attrs = new HashMap<String, Object>(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;
     }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java

@@ -142,12 +142,12 @@ public class IndelDBRateWalker extends RodWalker<OverlapTable,OverlapTabulator>
         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++;
             }
         }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java

@@ -601,7 +601,7 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
     public VCFWriter reduce(MendelianViolation variant, VCFWriter writer) {
         if ( variant != null ) {
             trioStructure.updateHomozygosityRegions(variant,bedOutput);
-            writer.add(variant.toVariantContext(), new byte[]{variant.getRefBase()});
+            writer.add(variant.toVariantContext(),variant.getRefBase());
         }
 
         return writer;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java

@@ -77,7 +77,7 @@ public class TestVariantContextWalker extends RodWalker<Integer, Integer> {
                         wroteHeader = true;
                     }
 
-                    writer.add(vc, new byte[]{ref.getBase()});
+                    writer.add(vc, ref.getBase());
                 }
 
                 n++;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java

@@ -126,7 +126,7 @@ public class VCF4WriterTestWalker extends RodWalker<Integer, Integer> {
             return 0;
 
         // Write directly variant context to VCF4.0 format.
-        vcfWriter.add(vc, ref.getBases());
+        vcfWriter.add(vc, ref.getBase());
 
         return 1;
     }

java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java

@@ -317,7 +317,7 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
 
 
 
-        vcfWriter.add(VariantContextUtils.modifyAttributes(filteredVC, attributes), new byte[]{ref.getBase()});
+        vcfWriter.add(VariantContextUtils.modifyAttributes(filteredVC, attributes), ref.getBase());
 
 
         return 1;

java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java

@@ -179,7 +179,7 @@ public class TrioGenotyperWalker extends RefWalker<VariantContext, Integer>{
             if ( a == 0 )
                 writer.writeHeader(VariantContextAdaptors.createVCFHeader(null, vc));
 
-            writer.add(vc, new byte[]{(byte)'.'});
+            writer.add(vc, (byte)'.');
             a++;
         }
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java

@@ -303,7 +303,7 @@ public class GenomicAnnotator extends RodWalker<LinkedList<VariantContext>, 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<LinkedList<VariantContext>, 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]);
             }
         }
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSelect.java

@@ -139,7 +139,7 @@ public class VariantSelect extends RodWalker<Integer, Integer> {
         }
 
         if ( someoneMatched )
-            writer.add(vc, new byte[]{ref.getBase()});
+            writer.add(vc, ref.getBase());
 
         return 1;
     }

java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSubset.java

@@ -73,7 +73,7 @@ public class VariantSubset extends RodWalker<Integer, Integer> {
 
             if ( (vc.isPolymorphic() || INCLUDE_NON_VARIANTS) &&
                     (!subset.isFiltered() || INCLUDE_FILTERED) )
-                writer.add(subset, new byte[]{ref.getBase()});
+                writer.add(subset, ref.getBase());
         }
 
         return 1;

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) {

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<Allele, String> alleleMap = new HashMap<Allele, String>(vc.getAlleles().size());

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),new Byte("A"));
-        writer.add(createVC(header),"A".getBytes());
+        writer.add(createVC(header),new Byte("A"));
         writer.close();
         VCFCodec reader = new VCFCodec();
         AsciiLineReader lineReader;