From 71d3e8e99b4ba368d28a414d12fcd633753fff05 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 25 Mar 2009 08:33:57 +0000
Subject: [PATCH] fixed another bug in gapped alignment computation

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@185 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/indels/SWPairwiseAlignment.java      | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/indels/SWPairwiseAlignment.java b/java/src/org/broadinstitute/sting/playground/indels/SWPairwiseAlignment.java
index 16079c8e5..de8f44ee8 100755
--- a/java/src/org/broadinstitute/sting/playground/indels/SWPairwiseAlignment.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/SWPairwiseAlignment.java
@@ -160,6 +160,7 @@ public class SWPairwiseAlignment {
             case DSTATE: o = CigarOperator.D; break;
         }
 
+        segment_length+=p.second;
         CigarElement e = new CigarElement(segment_length,o);
         lce.add(e);
         Collections.reverse(lce);
@@ -267,6 +268,7 @@ public class SWPairwiseAlignment {
             case ISTATE: o = CigarOperator.I; break;
             case DSTATE: o = CigarOperator.D; break;
         }
+        segment_length+=p.second;
         CigarElement e = new CigarElement(segment_length,o);
         lce.add(e);
         Collections.reverse(lce);
@@ -417,6 +419,7 @@ public void align3(String a, String b) {
             case ISTATE: o = CigarOperator.I; break;
             case DSTATE: o = CigarOperator.D; break;
         }
+        segment_length+=p.second;
         CigarElement e = new CigarElement(segment_length,o);
         lce.add(e);
         Collections.reverse(lce);
@@ -555,6 +558,7 @@ public void align3(String a, String b) {
                 case ISTATE: o = CigarOperator.I; break;
                 case DSTATE: o = CigarOperator.D; break;
             }
+            segment_length+=p.second;
             CigarElement e = new CigarElement(segment_length,o);
             lce.add(e);
             Collections.reverse(lce);
@@ -754,8 +758,13 @@ public void align3(String a, String b) {
         s2 = "AGACAGAGAAGG";
         testMe(s1,s2);
    */
-        String s1 = "CCAGCACACAGGTATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTTTTTTGA";
-        String s2 = "CCAGCACACATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTTTTTTGA";
+ //       String s1 = "CCAGCACACAGGTATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTTTTTTGA";
+ //       String s2 = "CCAGCACACATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTTTTTTGA";
+
+//        String s1 = "CCCATCTGTCTCCAATCTGCTGTTTTCCAAAAATTAGGGAACTTCAGTTTTCCCTTTGATACTCTGTATTTCTACCAACCACAACGCCAGGGCTGTCCTGCTTCTACAAGTGACAATGACAAATATAGGCCTGAAGGAAGATG";
+//        String s2 = "AAAATCTGTTTCCAATCTACTGTTTTCCAAAAATTAGGGAAGTTCAGTTTTCCCTTTGATACTCTGTTTCTACCAATCC";
+        String s1 = "CCCATCTGTCTCCAATCTGCTGTTTTCCAAAAATTAGGGAACTTCAGTTTTCCCTTTGATACTCTGTATTTCTACCAACCACAACGCCAGGGCTGTCCTGCTTCTACAAGTGACAATGACAAATATAGGCCTGAAGGAAGATG";
+        String s2 = "AAAATCTGTCTCCAATCTACTGTTTTCCAAAAATTAGGGAAGTTCAGTTTTCCCTTTGATACTCTGTTTCTACCAATCC";
            testMe(s1,s2);
     }