From a082b948a3a4993eee8ff742dfa7c4248f224189 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 14 Jan 2010 03:45:42 +0000
Subject: [PATCH] Support throughout for S and N cigar elements.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2579 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/AlignmentUtils.java           | 35 +++++++++++++------
 1 file changed, 25 insertions(+), 10 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/AlignmentUtils.java b/java/src/org/broadinstitute/sting/utils/AlignmentUtils.java
index f927547e8..30125cd62 100644
--- a/java/src/org/broadinstitute/sting/utils/AlignmentUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/AlignmentUtils.java
@@ -49,8 +49,14 @@ public class AlignmentUtils {
                             mm_count++;
                     }
                     break;
-                case I: i_read += ce.getLength(); break;
-                case D: i_ref += ce.getLength(); break;
+                case I:
+                case S:
+                    i_read += ce.getLength();
+                    break;
+                case D:
+                case N:
+                    i_ref += ce.getLength();
+                    break;
                 default: throw new RuntimeException("Unrecognized cigar element");
             }
 
@@ -86,9 +92,15 @@ public class AlignmentUtils {
                              mm_count++;
                     }
                     break;
-                case I: i_read += ce.getLength(); break;
-                case D: i_ref += ce.getLength(); break;
-                default: throw new RuntimeException("Unrecognized cigar element");
+                case I:
+                case S:
+                    i_read += ce.getLength();
+                    break;
+                case D:
+                case N:
+                    i_ref += ce.getLength();
+                    break;
+                default: throw new RuntimeException("Unrecognized cigar element: " + ce.getOperator());
             }
 
         }
@@ -143,12 +155,14 @@ public class AlignmentUtils {
                     }
                     break;
                 case I:
+                case S:
                     readIdx += ce.getLength();
                     break;
                 case D:
+                case N:
                     refIndex += ce.getLength();
                     break;
-                default: throw new StingException("Only M,I,D cigar elements are currently supported");
+                default: throw new StingException("The " + ce.getOperator() + " cigar element is not currently supported");
             }
 
         }
@@ -216,17 +230,18 @@ public class AlignmentUtils {
                     }
                     break;
                 case I:
+                case S:
                     readIndex += cigarElementLength;
                     break;
                 case D:
+                case N:
                     currentPos += cigarElementLength;
                     if ( currentPos > windowStart )
                         refIndex += Math.min(cigarElementLength, currentPos - windowStart);
                     break;
-                case S:
-                    readIndex += cigarElementLength;
-                    break;
-                default: throw new StingException("Only M,I,D,S cigar elements are currently supported; there was " + ce.getOperator());
+                default:
+                    // fail silently
+                    return 0;
             }
 
         }