Now can deal with input files that contain multiple copies of the same event. Only one assay sequence will be designed for each distinct variant, redundant variants will be discarded. Redundancy is defined as same start, same variant type, same ref and alt alleles (it does not matter, e.g., what the sample was as we do not record sample information anywhere).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5115 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -79,7 +79,9 @@ public class PickSequenomProbes extends RodWalker<String, String> {
     private GenomeLoc positionOfLastVariant = null;
 
     private int cnt = 0;
+    private int discarded = 0;
 
+    VariantCollection VCs ;  // will keep a set of distinct variants at a given site
     private List<GenomeLoc> processedVariantsInScope = new LinkedList<GenomeLoc>();
 
     public void initialize() {
@@ -101,6 +103,7 @@ public class PickSequenomProbes extends RodWalker<String, String> {
             }
 
 		}
+        VCs = new VariantCollection();
     }
 
 
@@ -110,7 +113,11 @@ public class PickSequenomProbes extends RodWalker<String, String> {
 
         logger.debug("Probing " + ref.getLocus() + " " + ref.getWindow());
 
-        Collection<VariantContext> VCs = tracker.getAllVariantContexts(ref);
+        VCs.clear();
+        VCs.addAll( tracker.getAllVariantContexts(ref), ref.getLocus() );
+
+        discarded += VCs.discarded();
+
         if ( VCs.size() == 0 )  {
             logger.debug("  Context empty");
             return "";
@@ -228,8 +235,8 @@ public class PickSequenomProbes extends RodWalker<String, String> {
                 assay_id.append("_");
                 assay_id.append(ref.getWindow().toString().replace(':', '_'));
             }
-
-            if ( addCounter ) assay_id.append("_"+(++cnt));
+            ++cnt;
+            if ( addCounter ) assay_id.append("_"+cnt);
 
             assaysForLocus.append(assay_id);
             assaysForLocus.append('\t');
@@ -269,5 +276,58 @@ public class PickSequenomProbes extends RodWalker<String, String> {
         return max+window-1;
     }
 
-    public void onTraversalDone(String sum) {}
+    public void onTraversalDone(String sum) {
+        logger.info(cnt+" assay seqences generated");
+        logger.info(discarded+" events were found to be duplicates and discarded (no redundant assays generated)");
+    }
+
+    static class EventComparator implements Comparator<VariantContext> {
+
+        public int compare(VariantContext o1, VariantContext o2) {
+            // if variants start at different positions, they are different. All we actually
+            // care about is detecting the variants that are strictly the same; the actual ordering of distinct variants
+            // (which one we deem less and which one greater) is utterly unimportant. We just need to be consistent.
+            if ( o1.getStart() < o2.getStart() ) return -1;
+            if ( o1.getStart() > o2.getStart() ) return 1;
+
+            if ( o1.getType() != o2.getType() ) return o1.getType().compareTo(o2.getType());
+
+            int refComp = o1.getReference().compareTo(o2.getReference());
+            if ( refComp != 0 ) return refComp;
+
+            return o1.getAlternateAllele(0).compareTo(o2.getAlternateAllele(0));
+
+        }
+    }
+
+    static class VariantCollection implements Iterable<VariantContext> {
+        TreeSet<VariantContext> variants = new TreeSet(new EventComparator());
+        int discarded = 0;
+
+        public void add(VariantContext vc, GenomeLoc current) {
+            if ( vc.getStart() != current.getStart() ) return; // we add only variants that start at current locus
+            // note that we do not check chr here, since the way this class is used, the mathod is always called with
+            // VCs coming from the same metadata tracker, so they simply can not be on different chrs!
+            if ( !vc.isBiallelic() ) {
+                logger.info("   Non-biallelic variant encountered; skipped");
+                return;
+            }
+            if ( variants.add(vc) == false ) discarded++;
+        }
+
+        public void addAll(Collection<VariantContext> c, GenomeLoc current) {
+            for ( VariantContext vc : c ) add(vc,current);
+        }
+
+        public void clear() {
+            variants.clear();
+            discarded = 0;
+        }
+
+        public int discarded() { return discarded; }
+
+        public int size() { return variants.size(); }
+
+        public Iterator<VariantContext> iterator() { return variants.iterator(); }
+    }
 }