adding the original allele list to a variant context (as the annotation ORIGINAL_ALLELE_LIST), in the case where the set alleles are the result of clipping. Added tests for both cases.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3658 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java

@@ -25,6 +25,9 @@ import java.util.*;
  */
 public class VCF4Codec implements FeatureCodec {
 
+    // a variant context flag for original allele strings
+    public static final String ORIGINAL_ALLELE_LIST = "ORIGINAL_ALLELE_LIST";
+
     // we have to store the list of strings that make up the header until they're needed
     private VCFHeader header = null;
 
@@ -364,6 +367,7 @@ public class VCF4Codec implements FeatureCodec {
      */
     private VariantContext parseVCFLine(String[] parts, boolean parseGenotypes) {
         try {
+            // increment the line count
             lineNo++;
             
             // parse out the required fields
@@ -376,15 +380,19 @@ public class VCF4Codec implements FeatureCodec {
             String filter = parts[6];
             String info = parts[7];
 
-
+            // get our alleles, filters, and setup an attribute map
             List<Allele> alleles = parseAlleles(ref, alts);
             Set<String> filters = parseFilters(filter);
             Map<String, Object> attributes = parseInfo(info, id);
 
             // find out our current location, and clip the alleles down to their minimum length
-            Pair<GenomeLoc, List<Allele>> locAndAlleles = (ref.length() > 1) ?
+            Pair<GenomeLoc, List<Allele>> locAndAlleles;
-                    clipAlleles(contig, pos, ref, alleles) :
+            if (ref.length() > 1) {
-                    new Pair<GenomeLoc, List<Allele>>(GenomeLocParser.createGenomeLoc(contig, pos), alleles);
+                    attributes.put(ORIGINAL_ALLELE_LIST,alleles);
+                    locAndAlleles = clipAlleles(contig, pos, ref, alleles);
+            } else {
+                    locAndAlleles = new Pair<GenomeLoc, List<Allele>>(GenomeLocParser.createGenomeLoc(contig, pos), alleles);
+            }
 
             // a map to store our genotypes
             Map<String, Genotype> genotypes = null;
@@ -477,7 +485,11 @@ public class VCF4Codec implements FeatureCodec {
 
     /**
      * clip the alleles, based on the reference
-     * @param unclippedAlleles the list of alleles
+     *
+     * @param contig our contig position
+     * @param position the unadjusted start position (pre-clipping)
+     * @param ref the reference string
+     * @param unclippedAlleles the list of unclipped alleles
      * @return a list of alleles, clipped to the reference
      */
     static Pair<GenomeLoc,List<Allele>> clipAlleles(String contig, long position, String ref, List<Allele> unclippedAlleles) {
@@ -502,7 +514,6 @@ public class VCF4Codec implements FeatureCodec {
             if (clipping) reverseClipped++;
         }
 
-        
         for (Allele a : unclippedAlleles)
             newAlleleList.add(Allele.create(Arrays.copyOfRange(a.getBases(),forwardClipping,a.getBases().length-reverseClipped),a.isReference()));
 

java/test/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4UnitTest.java

@@ -41,7 +41,7 @@ public class VCF4UnitTest extends BaseTest {
         } catch (FileNotFoundException e) {
             throw new StingException("unable to load the sequence dictionary");
         }
-        GenomeLocParser.setupRefContigOrdering(seq);
+        GenomeLocParser.setupRefContigOrdering(seq.getSequenceDictionary());
     }
 
     @Test
@@ -197,13 +197,33 @@ public class VCF4UnitTest extends BaseTest {
     }
     
     // test too few info lines, we don't provide the DP in this line
-    String twoFewInfoLine = "20\t14370\trs6054257\tG\tA\t29\tPASS\tNS=3;AF=0.5;DB;H2\tGT:GQ:DP:HQ\t0|0:48:1:51,51\t0|0:48:1:51,51\t0|0:48:1:51,51";
+    String twoFewInfoLine = "20\t14370\trs6054257\tG\tA\t29\tPASS\tNS=3;AF=0.5;DB\tGT:GQ:DP:HQ\t0|0:48:1:51,51\t0|0:48:1:51,51\t0|0:48:1:51,51";
     @Test
     public void testCheckTwoFewInfoValidation() {
         TestSetup testSetup = new TestSetup().invoke(vcfGenotypeFile);
         testSetup.codec.decode(twoFewInfoLine);
     }
 
+    // test that the variant context adds attributes for the original alleles when clipped
+    String clippedAlleleLine = "20\t14370\trs6054257\tGGG\tG\t29\tPASS\tNS=3;AF=0.5;DB;H2\tGT:GQ:DP:HQ\t0|1:48:1:51,51\t0|0:48:1:51,51\t0|0:48:1:51,51";
+    @Test
+    public void testClippedAllelesAddedAsAnnotation() {
+        TestSetup testSetup = new TestSetup().invoke(vcfGenotypeFile);
+        VariantContext context = (VariantContext)testSetup.codec.decode(clippedAlleleLine);
+        Assert.assertTrue(context.hasAttribute(VCF4Codec.ORIGINAL_ALLELE_LIST));
+        List<Allele> alleles = (List<Allele>)context.getAttribute(VCF4Codec.ORIGINAL_ALLELE_LIST);
+        Assert.assertEquals("Expected allele list of 2, got " + alleles.size(),2,alleles.size());
+        Assert.assertTrue(alleles.get(0).basesMatch("GGG"));
+        Assert.assertTrue(alleles.get(1).basesMatch("G"));
+    }
+    // test that when we don't clip the alleles, we don't see the annotation
+    @Test
+    public void testNoClippedAllelesNoAddedAsAnnotation() {
+        TestSetup testSetup = new TestSetup().invoke(vcfGenotypeFile);
+        VariantContext context = (VariantContext)testSetup.codec.decode(twoFewInfoLine);
+        Assert.assertTrue(!context.hasAttribute(VCF4Codec.ORIGINAL_ALLELE_LIST));
+    }
+
     // test that we're getting the right genotype for a multi-base polymorphism
     String MNPLine = "20\t14370\trs6054257\tGG\tAT\t29\tPASS\tNS=3;DP=14;AF=0.5;DB;H2\tGT:GQ:DP:HQ\t0|0:48:1:51,51\t1|0:48:8:51,51\t1/1:43:5:.,.";
     @Test