From f5a301fb6354f0f3fad6cd01bd1c154ee15a1086 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Tue, 23 Apr 2013 18:26:20 -0400
Subject: [PATCH] Bugfix for AlignmentUtils.trimCigarByBases

-- Previous version would trim down 2M2D2M into 2M if you asked for the first 2 bases, but this can result in incorrect alignment of the bases to the reference as the bases no longer span the full reference interval expected.  Fixed and added unit tests
---
 .../org/broadinstitute/sting/utils/sam/AlignmentUtils.java    | 4 ++--
 .../sting/utils/sam/AlignmentUtilsUnitTest.java               | 3 ++-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
index 59a22c550..fa35e3f53 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
@@ -934,7 +934,7 @@ public final class AlignmentUtils {
      */
     public static Cigar trimCigarByBases(final Cigar cigar, final int start, final int end) {
         if ( start < 0 ) throw new IllegalArgumentException("Start must be >= 0 but got " + start);
-        if ( end < start ) throw new IllegalArgumentException("End " + end + " is < start start " + start);
+        if ( end < start ) throw new IllegalArgumentException("End " + end + " is < start = " + start);
         if ( end > cigar.getReadLength() ) throw new IllegalArgumentException("End is beyond the cigar's read length " + end + " for cigar " + cigar );
 
         final Cigar result = trimCigar(cigar, start, end, false);
@@ -962,7 +962,7 @@ public final class AlignmentUtils {
 
         int pos = 0;
         for ( final CigarElement elt : cigar.getCigarElements() ) {
-            if ( pos > end ) break;
+            if ( pos > end && (byReference || elt.getOperator() != CigarOperator.D) ) break;
 
             switch ( elt.getOperator() ) {
                 case D:
diff --git a/public/java/test/org/broadinstitute/sting/utils/sam/AlignmentUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/sam/AlignmentUtilsUnitTest.java
index 2a2d80206..e7d54c460 100644
--- a/public/java/test/org/broadinstitute/sting/utils/sam/AlignmentUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/sam/AlignmentUtilsUnitTest.java
@@ -792,7 +792,8 @@ public class AlignmentUtilsUnitTest {
         tests.add(new Object[]{"2M2D2I", 3, 3, "1I"});
         tests.add(new Object[]{"2M2D2I", 2, 2, "2D1I"});
         tests.add(new Object[]{"2M2D2I", 1, 2, "1M2D1I"});
-        tests.add(new Object[]{"2M2D2I", 1, 1, "1M"});
+        tests.add(new Object[]{"2M2D2I", 0, 1, "2M2D"});
+        tests.add(new Object[]{"2M2D2I", 1, 1, "1M2D"});
 
         return tests.toArray(new Object[][]{});
     }