From 9a60e72364724a2f4d27fd14dfee8e86c3ded76c Mon Sep 17 00:00:00 2001
From: delangel <delangel@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 29 Oct 2010 02:03:36 +0000
Subject: [PATCH] Trivial change to LeftAlignVariants: make walker return
 number of aligned variants on map(), and print out the # of aligned variants
 at the end of the traversal.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4595 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../variantutils/LeftAlignVariants.java       | 37 ++++++++++++-------
 1 file changed, 24 insertions(+), 13 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
index e8c6dd566..851bf98fa 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
@@ -76,26 +76,35 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
             return 0;
 
         Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", null, context.getLocation(), true, false);
-        for ( VariantContext vc : VCs )
-            alignAndWrite(vc, ref);
 
-        return 0;
+        int changedSites = 0;
+        for ( VariantContext vc : VCs )
+            changedSites += alignAndWrite(vc, ref);
+
+        return changedSites;
     }
 
     public Integer reduceInit() { return 0; }
 
-    public Integer reduce(Integer value, Integer sum) { return 0; }
-
-    public void onTraversalDone(Integer result) {}
-
-    private void alignAndWrite(VariantContext vc, final ReferenceContext ref) {
-        if ( vc.isBiallelic() && vc.isIndel() )
-            writeLeftAlignedIndel(vc, ref);
-        else
-            writer.add(vc, ref.getBase());
+    public Integer reduce(Integer value, Integer sum) {
+        return sum + value;
     }
 
-    private void writeLeftAlignedIndel(final VariantContext vc, final ReferenceContext ref) {
+    public void onTraversalDone(Integer result) {
+        System.out.println(result + " variants were aligned");
+    }
+
+
+    private int alignAndWrite(VariantContext vc, final ReferenceContext ref) {
+        if ( vc.isBiallelic() && vc.isIndel() )
+            return writeLeftAlignedIndel(vc, ref);
+        else {
+            writer.add(vc, ref.getBase());
+            return 0;
+        }
+    }
+
+    private int writeLeftAlignedIndel(final VariantContext vc, final ReferenceContext ref) {
         final byte[] refSeq = ref.getBases();
 
         // get the indel length
@@ -133,8 +142,10 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
             newVC = updateAllele(newVC, newAllele);
 
             writer.add(newVC, refSeq[indelIndex-1]);
+            return 1;
         } else {
             writer.add(vc, ref.getBase());
+            return 0;
         }
     }