From 83300582161dd08d76a19c62adf0ed4040ebefcc Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 29 Dec 2009 22:41:58 +0000
Subject: [PATCH] method added: getEventStringsWithCounts() Returns list of
 Pairs <String,Integer>, where each pair consists of a unique indel event
 observed at the site and the total number of observations of that event.
 String representation for insertions is verbose (e.g. +ACT), while deletions
 are represented as "5D" (since read backed pileup has no reference
 information, so we can not get actual sequence of deleted bases)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2479 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../pileup/ReadBackedExtendedEventPileup.java | 32 +++++++++++++++++--
 1 file changed, 30 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
index 7885681db..c0d660975 100644
--- a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
+++ b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
@@ -2,8 +2,7 @@ package org.broadinstitute.sting.utils.pileup;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.gatk.iterators.IterableIterator;
+import org.broadinstitute.sting.utils.Pair;
 
 import java.util.*;
 
@@ -290,6 +289,35 @@ public class ReadBackedExtendedEventPileup implements Iterable<ExtendedEventPile
         return v;
     }
 
+    public List<Pair<String,Integer>> getEventStringsWithCounts() {
+        Map<String, Integer> events = new HashMap<String,Integer>();
+
+        for ( ExtendedEventPileupElement e : this ) {
+            Integer cnt;
+            String indel = null;
+            switch ( e.getType() ) {
+                case INSERTION:
+                    indel = "+"+e.getEventBases();
+                    break;
+                case DELETION:
+                    indel = Integer.toString(e.getEventLength())+"D";
+                    break;
+                case NOEVENT: continue;
+                default: throw new StingException("Unknown event type encountered: "+e.getType());
+            }
+
+            cnt = events.get(indel);
+            if ( cnt == null ) events.put(indel,1);
+            else events.put(indel,cnt.intValue()+1);
+        }
+
+        List<Pair<String,Integer>> eventList = new ArrayList<Pair<String,Integer>>(events.size());
+        for ( Map.Entry<String,Integer> m : events.entrySet() ) {
+            eventList.add( new Pair<String,Integer>(m.getKey(),m.getValue()));
+        }
+        return eventList;
+    }
+
 
     /**
      * Get an array of the mapping qualities