From e8d544869d1a0d9f026a40e284c11d2c4e805e88 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sat, 12 Sep 2009 19:11:38 +0000
Subject: [PATCH] Alignment context now supports the idea of skipped bases --
 not currently in use

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1598 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/contexts/AlignmentContext.java | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
index c6ed4d6a4..9e3fbec81 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
@@ -45,6 +45,12 @@ public class AlignmentContext {
     protected List<SAMRecord> reads = null;
     protected List<Integer> offsets = null;
 
+    /**
+     * The number of bases we've skipped over in the reference since the last map invocation.
+     * Only filled in by RodTraversals right now.  By default, nothing is being skipped, so skippedBases == 0.
+     */
+    private long skippedBases = 0;
+
     /**
      * Default constructor for AlignmentContext object
      * since private objects are already set to null we
@@ -70,6 +76,14 @@ public class AlignmentContext {
         this.offsets = offsets;
     }
 
+    public AlignmentContext(GenomeLoc loc, List<SAMRecord> reads, List<Integer> offsets, long skippedBases ) {
+        this.loc = loc;
+        this.reads = reads;
+        this.offsets = offsets;
+        this.skippedBases = skippedBases;
+    }
+
+
     /**
      * get all of the reads within this context
      * 
@@ -184,4 +198,14 @@ public class AlignmentContext {
 
         return new AlignmentContext(ac.getLocation(), reads, offsets);
     }
+
+    /**
+     * Returns the number of bases we've skipped over in the reference since the last map invocation.
+     * Only filled in by RodTraversals right now.  A value of 0 indicates that no bases were skipped.
+     *
+     * @return the number of skipped bases
+     */
+    public long getSkippedBases() {
+        return skippedBases;
+    }
 }