From 489c15b99d29907f1c864cac87f434a5e7294cbf Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Mon, 15 Aug 2011 01:42:34 -0400
Subject: [PATCH] Fixed indexing issue in coordinate conversion

When a read had been previously soft clipped, the UnclippedEnd could not be used directly as Reference Coordinate for clipping , because the read does not go that far.
---
 .../sting/utils/clipreads/ReadClipper.java            | 11 +++++++----
 .../org/broadinstitute/sting/utils/sam/ReadUtils.java |  6 +++---
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
index 1307f1b6f..00405a98c 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
@@ -3,6 +3,7 @@ package org.broadinstitute.sting.utils.clipreads;
 import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.SAMRecord;
+import org.broad.tribble.util.PositionalStream;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.jets3t.service.multi.ThreadedStorageService;
 
@@ -48,8 +49,10 @@ public class ReadClipper {
     }
 
     public SAMRecord hardClipByReferenceCoordinates(int refStart, int refStop) {
-        int start = ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart);
-        int stop = ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop);
+        int start = (refStart < 0) ? 0 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart);
+        int stop = (refStop < 0) ? read.getReadLength()-1 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop);
+
+        System.out.println("DEBUG -- clipping start/stop: " + start + "/" + stop);
         this.addOp(new ClippingOp(start, stop));
         return clipRead(ClippingRepresentation.HARDCLIP_BASES);
     }
@@ -60,9 +63,9 @@ public class ReadClipper {
     }
 
     public SAMRecord hardClipBothEndsByReferenceCoordinates(int left, int right) {
-        this.read = hardClipByReferenceCoordinates(read.getUnclippedStart(), left);
+        this.read = hardClipByReferenceCoordinates(-1, left);
         this.ops = null; // reset the operations
-        return hardClipByReferenceCoordinates(right, read.getUnclippedEnd());
+        return hardClipByReferenceCoordinates(right, -1);
     }
 
     /**
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 3d803804a..5d39a01a5 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -650,13 +650,13 @@ public class ReadUtils {
             return ReadAndIntervalOverlap.RIGHT_OVERLAP;
     }
 
-    @Requires({"refCoord >= read.getUnclippedStart()", "refCoord <= read.getUnclippedEnd()"})
+    @Requires({"refCoord >= read.getAlignmentStart()", "refCoord <= read.getAlignmentEnd()"})
     @Ensures({"result >= 0", "result < read.getReadLength()"})
     public static int getReadCoordinateForReferenceCoordinate(SAMRecord read, int refCoord) {
         int readBases = 0;
         int refBases = 0;
-        int goal = refCoord - read.getUnclippedStart();  // read coords are 0-based!
-        boolean goalReached = false;
+        int goal = refCoord - read.getAlignmentStart();  // read coords are 0-based!
+        boolean goalReached = refBases == goal;
 
         Iterator<CigarElement> cigarElementIterator = read.getCigar().getCigarElements().iterator();
         while (!goalReached && cigarElementIterator.hasNext()) {