From cba5f055383bfa315b4ab3fc384f4c9ed820e33a Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 24 Aug 2010 20:48:25 +0000
Subject: [PATCH] Small fixes for consistency in the numbers.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4103 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../oneoffprojects/walkers/IndelConsistencyReadCounter.java  | 5 ++++-
 .../sting/oneoffprojects/walkers/RealignedReadCounter.java   | 4 +++-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java
index 66c150ca0..abff66830 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java
@@ -97,6 +97,10 @@ public class IndelConsistencyReadCounter extends ReadWalker<Integer, Integer> {
     private static boolean containsIndel(final SAMRecord r, final VariantContext vc) {
         int indelStart = vc.getStart() + 1;
         int readPos = r.getAlignmentStart();
+
+        if ( vc.isInsertion() && indelStart == readPos )
+            return true;
+
         final Cigar cigar = r.getCigar();
 
         int idx = 0;
@@ -106,7 +110,6 @@ public class IndelConsistencyReadCounter extends ReadWalker<Integer, Integer> {
             switch ( ce.getOperator() ) {
                 case M:
                 case I:
-                case S:
                     readPos += ce.getLength();
                     break;
                 default:
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/RealignedReadCounter.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/RealignedReadCounter.java
index e6688c691..03777e8ec 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/RealignedReadCounter.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/RealignedReadCounter.java
@@ -109,7 +109,9 @@ public class RealignedReadCounter extends ReadWalker<Integer, Integer> {
 
     private int getIndelSize(SAMRecord read) {
         for ( CigarElement ce : read.getCigar().getCigarElements() ) {
-            if ( ce.getOperator() == CigarOperator.I || ce.getOperator() == CigarOperator.D )
+            if ( ce.getOperator() == CigarOperator.I )
+                return 0;
+            if ( ce.getOperator() == CigarOperator.D )
                 return ce.getLength();
         }
         logger.warn("We didn't see an indel for this read: " + read.getReadName() + " " + read.getAlignmentStart() + " " + read.getCigar());