Working implementation of BCF2

-- Nearly complete on spec implementation.  Slow but clean
-- Some refactoring of VariantContext to support common functions for BCF and VCF

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java

@@ -278,7 +278,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
         getters.put("REF", new Getter() {
             public String get(VariantContext vc) {
                 StringBuilder x = new StringBuilder();
-                x.append(getAlleleDisplayString(vc, vc.getReference()));
+                x.append(vc.getAlleleWithRefPadding(vc.getReference()));
                 return x.toString();
             }
         });
@@ -290,7 +290,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
 
                 for ( int i = 0; i < n; i++ ) {
                     if ( i != 0 ) x.append(",");
-                    x.append(getAlleleDisplayString(vc, vc.getAlternateAllele(i)));
+                    x.append(vc.getAlleleWithRefPadding(vc.getAlternateAllele(i)));
                 }
                 return x.toString();
             }
@@ -329,22 +329,14 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
         }});
     }
     
-    private static String getAlleleDisplayString(VariantContext vc, Allele allele) {
-        StringBuilder sb = new StringBuilder();
-        if ( vc.hasReferenceBaseForIndel() && !vc.isSNP() )
-            sb.append((char)vc.getReferenceBaseForIndel().byteValue());
-        sb.append(allele.getDisplayString());
-        return sb.toString();
-    }
-    
     private static Object splitAltAlleles(VariantContext vc) {
         final int numAltAlleles = vc.getAlternateAlleles().size();
         if ( numAltAlleles == 1 )
-            return getAlleleDisplayString(vc, vc.getAlternateAllele(0));
+            return vc.getAlleleWithRefPadding(vc.getAlternateAllele(0));
 
         final List<String> alleles = new ArrayList<String>(numAltAlleles);
         for ( Allele allele : vc.getAlternateAlleles() )
-            alleles.add(getAlleleDisplayString(vc, allele));
+            alleles.add(vc.getAlleleWithRefPadding(allele));
         return alleles;
     }
 }

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java

@@ -611,7 +611,7 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
             alleles.add(allele);
     }
 
-    protected static boolean isSingleNucleotideEvent(List<Allele> alleles) {
+    public static boolean isSingleNucleotideEvent(List<Allele> alleles) {
         for ( Allele a : alleles ) {
             if ( a.length() != 1 )
                 return false;
@@ -683,7 +683,7 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
      * @param lineNo the current line number in the file
      * @return the new reference end position of this event
      */
-    protected static int clipAlleles(int position, String ref, List<Allele> unclippedAlleles, List<Allele> clippedAlleles, int lineNo) {
+    public static int clipAlleles(int position, String ref, List<Allele> unclippedAlleles, List<Allele> clippedAlleles, int lineNo) {
 
         int forwardClipping = computeForwardClipping(unclippedAlleles, (byte)ref.charAt(0));
         int reverseClipping = computeReverseClipping(unclippedAlleles, ref.getBytes(), forwardClipping, false, lineNo);

public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java

@@ -519,6 +519,17 @@ public class VariantContext implements Feature { // to enable tribble integratio
         return REFERENCE_BASE_FOR_INDEL;
     }
 
+    public String getAlleleWithRefPadding(final Allele allele) {
+        if ( hasReferenceBaseForIndel() && isIndel() ) {
+            StringBuilder sb = new StringBuilder();
+            sb.append((char)getReferenceBaseForIndel().byteValue());
+            sb.append(allele.getDisplayString());
+            return sb.toString();
+        } else
+            return allele.getDisplayString();
+    }
+
+
     // ---------------------------------------------------------------------------------------------------------
     //
     // get routines to access context info fields

public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java

@@ -384,6 +384,10 @@ public class VariantContextBuilder {
         return this;
     }
 
+    public long getStart() {
+        return start;
+    }
+
     /**
      * Tells us that the resulting VariantContext should have the specified contig stop
      * @param stop

public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java

@@ -171,21 +171,33 @@ public class VariantContextUtils {
         return new Genotype(g.getSampleName(), g.getAlleles(), g.getLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, attrs, g.isPhased());
     }
 
-    public static VariantContext createVariantContextWithPaddedAlleles(VariantContext inputVC, boolean refBaseShouldBeAppliedToEndOfAlleles) {
+    /**
-        // see if we need to pad common reference base from all alleles
+     * Returns true if the alleles in inputVC should have reference bases added for padding
-        boolean padVC = false;
+     *
-
+     * We need to pad a VC with a common base if the length of the reference allele is
-        // We need to pad a VC with a common base if the length of the reference allele is less than the length of the VariantContext.
+     * less than the length of the VariantContext. This happens because the position of
-        // This happens because the position of e.g. an indel is always one before the actual event (as per VCF convention).
+     * e.g. an indel is always one before the actual event (as per VCF convention).
+     *
+     * @param inputVC the VC to evaluate, cannot be null
+     * @return true if
+     */
+    public static boolean needsPadding(final VariantContext inputVC) {
         final int recordLength = inputVC.getEnd() - inputVC.getStart() + 1;
         final int referenceLength = inputVC.getReference().length();
+
         if ( referenceLength == recordLength )
-            padVC = false;
+            return false;
         else if ( referenceLength == recordLength - 1 )
-            padVC = true;
+            return true;
         else if ( !inputVC.hasSymbolicAlleles() )
             throw new IllegalArgumentException("Badly formed variant context at location " + String.valueOf(inputVC.getStart()) +
                     " in contig " + inputVC.getChr() + ". Reference length must be at most one base shorter than location size");
+        else
+            return false;
+    }
+
+    public static VariantContext createVariantContextWithPaddedAlleles(VariantContext inputVC, boolean refBaseShouldBeAppliedToEndOfAlleles) {
+        final boolean padVC = needsPadding(inputVC);
 
         // nothing to do if we don't need to pad bases
         if ( padVC ) {