From 0cd9438ac2225eea9dc629e49bf79d538b88a837 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Tue, 30 Aug 2011 02:31:00 -0400
Subject: [PATCH] fixed soft unclipped calculation

* getRefCoordSoftUnclippedEnd was not resetting the shift when hitting insertions. Fixed.
* getReadCoordinateForReferenceCoordinateBeforeAlignmentEnd was returning the wrong read coordinate position. Fixed.
---
 .../src/org/broadinstitute/sting/utils/sam/ReadUtils.java   | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
index 7d02c8d3b..62bbb0307 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -680,6 +680,8 @@ public class ReadUtils {
             lastOperator = cigarElement.getOperator();
             if (cigarElement.getOperator().consumesReferenceBases() || cigarElement.getOperator() == CigarOperator.SOFT_CLIP || cigarElement.getOperator() == CigarOperator.HARD_CLIP)
                 shift = cigarElement.getLength();
+            else
+                shift = 0;
         }
         return (lastOperator == CigarOperator.HARD_CLIP) ? stop-1 : stop+shift-1 ;
     }
@@ -710,8 +712,8 @@ public class ReadUtils {
      */
     @Requires({"refCoord <= read.getUnclippedEnd()", "refCoord > read.getAlignmentEnd()"})
     private static int getReadCoordinateForReferenceCoordinateBeforeAlignmentEnd(SAMRecord read, int refCoord) {
-        if (getRefCoordSoftUnclippedEnd(read) > refCoord)
-            return refCoord - read.getAlignmentEnd() + 1;
+        if (getRefCoordSoftUnclippedEnd(read) >= refCoord)
+            return refCoord - getRefCoordSoftUnclippedStart(read) + 1;
         return -1;
     }