From 85ca68fab6989766177a5f889564af981d646728 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 31 Aug 2009 18:39:19 +0000
Subject: [PATCH] Initial version: creates a packed file from a fasta, suitable
 for consumption by BWT-SW.  Works with E coli fasta, but will not work at
 this moment with multi-chr fastas. Will be made into a utility routine when
 BWA comes together.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1494 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/bwa/CreatePACFromReference.java     | 107 ++++++++++++++++++
 1 file changed, 107 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/bwa/CreatePACFromReference.java

diff --git a/java/src/org/broadinstitute/sting/bwa/CreatePACFromReference.java b/java/src/org/broadinstitute/sting/bwa/CreatePACFromReference.java
new file mode 100755
index 000000000..1ad3f649c
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/bwa/CreatePACFromReference.java
@@ -0,0 +1,107 @@
+/*
+ * Copyright (c) 2009 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.bwa;
+
+import net.sf.picard.reference.ReferenceSequenceFile;
+import net.sf.picard.reference.ReferenceSequenceFileFactory;
+import net.sf.picard.reference.ReferenceSequence;
+
+import java.io.*;
+
+import org.broadinstitute.sting.utils.StingException;
+
+/**
+ * Generate a .PAC file from a given reference.
+ *
+ * @author hanna
+ * @version 0.1
+ */
+
+public class CreatePACFromReference {
+    private static final int ALPHABET_SIZE = 4;
+
+    public static void main( String argv[] ) throws FileNotFoundException, IOException {
+        if( argv.length != 1 ) {
+            System.out.println("No reference");
+            return;
+        }
+
+        // Read in the first sequence in the input file
+        String inputFileName = argv[0];
+        File inputFile = new File(inputFileName);
+        ReferenceSequenceFile reference = ReferenceSequenceFileFactory.getReferenceSequenceFile(inputFile);
+        ReferenceSequence sequence = reference.nextSequence();
+
+        // Target file for output
+        File outputFile = new File(inputFileName + ".mypac");
+        BufferedOutputStream outputStream = new BufferedOutputStream(new FileOutputStream(outputFile));
+
+        // Number of bytes, rounded up, plus one extra byte indicating how many bases the last byte holds.
+        byte packed = 0;
+        int positionInPack = 0;
+
+        for( byte base: sequence.getBases() ) {
+            // Pack base into the appropriate bits of the byte.
+            packed |= (getPackedRepresentation(base) << 2*(ALPHABET_SIZE-positionInPack-1));
+
+            // Increment the packed counter.  If all possible bases have been squeezed into this byte, write it out.
+            positionInPack = ++positionInPack % 4;
+            if( positionInPack == 0 ) {
+                outputStream.write(packed);
+                packed = 0;
+            }
+        }
+
+        // Last (incomplete) block in file.
+        if( positionInPack > 0 )
+            outputStream.write(packed);
+
+        // Last character of a .pac file is how many bases are in the last byte.
+        outputStream.write(positionInPack);
+        
+        outputStream.close();
+    }
+
+    /**
+     * Gets the two-bit representation of a base.  A=00b, C=01b, G=10b, T=11b.
+     * @param base ASCII value for the base to pack.
+     * @return A byte from 0-3 indicating the base's packed value.
+     */
+    private static byte getPackedRepresentation(byte base) {
+        switch( base ) {
+            case 'A':
+                return 0;
+            case 'C':
+                return 1;
+            case 'G':
+                return 2;
+            case 'T':
+                return 3;
+            default:
+                throw new StingException("Unknown base type: " + base);
+        }
+    }
+}