From 522f8b58be66568a7868adce3dc42da3b218b39c Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 8 May 2009 22:18:04 +0000
Subject: [PATCH] Added second method for getting large sequences of the
 reference for use in reads traversals.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@645 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../providers/ReferenceProvider.java          | 46 ++++++++++++++++---
 1 file changed, 40 insertions(+), 6 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceProvider.java b/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceProvider.java
index f2e088a49..f61595b01 100755
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceProvider.java
+++ b/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceProvider.java
@@ -5,6 +5,7 @@ import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
 import edu.mit.broad.picard.reference.ReferenceSequence;
 import net.sf.samtools.util.StringUtil;
+import net.sf.samtools.SAMRecord;
 
 /**
  * Created by IntelliJ IDEA.
@@ -14,10 +15,49 @@ import net.sf.samtools.util.StringUtil;
  * To change this template use File | Settings | File Templates.
  */
 public class ReferenceProvider {
+    private IndexedFastaSequenceFile sequenceFile;
+    private Shard shard;
+
+    // Lazy
     private ReferenceSequence referenceSequence;
     private GenomeLoc referenceInterval;
 
     public ReferenceProvider( IndexedFastaSequenceFile sequenceFile, Shard shard ) {
+        this.sequenceFile = sequenceFile;
+        this.shard = shard;
+    }
+
+    public char getReferenceBase( GenomeLoc genomeLoc ) throws InvalidPositionException {
+        if( referenceSequence == null )
+            lazyInitializeLocusAccess();            
+
+        validateLocation( genomeLoc );
+        int offset = (int)(genomeLoc.getStart() - referenceInterval.getStart());
+        return StringUtil.bytesToString( referenceSequence.getBases(), offset, 1 ).charAt(0);
+    }
+
+    /**
+     * Gets the bases of the reference that are aligned to the given read.
+     * @param read the read for which to extract reference information.
+     * @return The bases corresponding to this read, or null if the read is unmapped.
+     */
+    public char[] getReferenceBases( SAMRecord read ) {
+        if( read.getReadUnmappedFlag() )
+            return null;
+
+        String contig = read.getReferenceName();
+        int start = read.getAlignmentStart();
+        int stop = read.getAlignmentEnd();
+
+        ReferenceSequence alignmentToReference = sequenceFile.getSubsequenceAt( contig, start, stop );
+        return StringUtil.bytesToString(alignmentToReference.getBases()).toCharArray();
+    }
+
+    /**
+     * Perform a lazy initialization of access to the locus.  Sets up the reference sequence and
+     * limits the user to work only at that sequence.
+     */
+    private void lazyInitializeLocusAccess() {
         GenomeLoc position = shard.getGenomeLoc();
         this.referenceSequence = sequenceFile.getSubsequenceAt( position.getContig(),
                                                                 position.getStart(),
@@ -25,12 +65,6 @@ public class ReferenceProvider {
         this.referenceInterval = position;
     }
 
-    public char getReferenceBase( GenomeLoc genomeLoc ) throws InvalidPositionException {
-        validateLocation( genomeLoc );
-        int offset = (int)(genomeLoc.getStart() - referenceInterval.getStart());
-        return StringUtil.bytesToString( referenceSequence.getBases(), offset, 1 ).charAt(0);
-    }
-
     /**
      * Validates that the genomeLoc is one base wide and is in the reference sequence.
      * @param genomeLoc location to verify.