From f06f955e06d066933d99f23ca75783cb2d32df1c Mon Sep 17 00:00:00 2001
From: fromer <fromer@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 22 Oct 2010 20:11:15 +0000
Subject: [PATCH] Added count of number of mergeable records (within specified
 distance cutoff)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4560 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../MergePhasedSegregatingPolymorphismsToMNPvcfWriter.java | 7 +++++++
 .../phasing/MergeSegregatingPolymorphismsWalker.java       | 1 +
 2 files changed, 8 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingPolymorphismsToMNPvcfWriter.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingPolymorphismsToMNPvcfWriter.java
index 3b0a5eb4d..f17d41408 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingPolymorphismsToMNPvcfWriter.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingPolymorphismsToMNPvcfWriter.java
@@ -46,6 +46,7 @@ public class MergePhasedSegregatingPolymorphismsToMNPvcfWriter implements VCFWri
 
     private VCFRecord vcfrWaitingToMerge;
     private List<VCFRecord> filteredVcfrList;
+    private int numRecordsWithinDistance;
     private int numMergedRecords;
 
     private Logger logger;
@@ -59,6 +60,7 @@ public class MergePhasedSegregatingPolymorphismsToMNPvcfWriter implements VCFWri
         this.maxGenomicDistanceForMNP = maxGenomicDistanceForMNP;
         this.vcfrWaitingToMerge = null;
         this.filteredVcfrList = new LinkedList<VCFRecord>();
+        this.numRecordsWithinDistance = 0;
         this.numMergedRecords = 0;
         this.logger = logger;
         this.takeOwnershipOfInner = takeOwnershipOfInner;
@@ -108,6 +110,7 @@ public class MergePhasedSegregatingPolymorphismsToMNPvcfWriter implements VCFWri
             else { // waiting to merge vcfrWaitingToMerge, and curVcIsNotFiltered. So, attempt to merge them:
                 boolean mergedRecords = false;
                 if (minDistance(vcfrWaitingToMerge.vc, vc) <= maxGenomicDistanceForMNP) {
+                    numRecordsWithinDistance++;
                     VariantContext mergedVc = VariantContextUtils.mergeIntoMNP(vcfrWaitingToMerge.vc, vc, referenceFileForMNPmerging);
                     if (mergedVc != null) {
                         mergedRecords = true;
@@ -139,6 +142,10 @@ public class MergePhasedSegregatingPolymorphismsToMNPvcfWriter implements VCFWri
         filteredVcfrList.clear();
     }
 
+    public int getNumMergeableRecordsWithinDistance() {
+        return numRecordsWithinDistance;
+    }
+
     public int getNumMergedRecords() {
         return numMergedRecords;
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingPolymorphismsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingPolymorphismsWalker.java
index 4e54c3c2c..f922f89c7 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingPolymorphismsWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingPolymorphismsWalker.java
@@ -134,6 +134,7 @@ public class MergeSegregatingPolymorphismsWalker extends RodWalker<Integer, Inte
      */
     public void onTraversalDone(Integer result) {
         vcMergerWriter.close();
+        System.out.println("Number of potentially merged records (distance <= "+ maxGenomicDistanceForMNP + "): " + vcMergerWriter.getNumMergeableRecordsWithinDistance());        
         System.out.println("Number of records merged: " + vcMergerWriter.getNumMergedRecords());
     }
 }
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