On the road to human: make sure the suffix array will fit in a Java array.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1846 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWT.java

@@ -2,7 +2,6 @@ package org.broadinstitute.sting.alignment.bwa.bwt;
 
 import org.broadinstitute.sting.alignment.bwa.packing.PackUtils;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.Pair;
 
 /**
  * Represents the Burrows-Wheeler Transform of a reference sequence.

java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWTReader.java

@@ -17,7 +17,7 @@ public class BWTReader {
     /**
      * Input stream from which to read BWT data.
      */
-    private InputStream inputStream;
+    private FileInputStream inputStream;
 
     /**
      * Create a new BWT reader.
@@ -25,7 +25,7 @@ public class BWTReader {
      */
     public BWTReader( File inputFile ) {
         try {
-            this.inputStream = new BufferedInputStream(new FileInputStream(inputFile));
+            this.inputStream = new FileInputStream(inputFile);
         }
         catch( FileNotFoundException ex ) {
             throw new StingException("Unable to open input file", ex);

java/src/org/broadinstitute/sting/alignment/bwa/bwt/SuffixArrayReader.java

@@ -17,7 +17,7 @@ public class SuffixArrayReader {
     /**
      * Input stream from which to read suffix array data.
      */
-    private InputStream inputStream;
+    private FileInputStream inputStream;
 
     /**
      * BWT to use to fill in missing data.
@@ -31,7 +31,7 @@ public class SuffixArrayReader {
      */
     public SuffixArrayReader(File inputFile, BWT bwt) {
         try {
-            this.inputStream = new BufferedInputStream(new FileInputStream(inputFile));
+            this.inputStream = new FileInputStream(inputFile);
             this.bwt = bwt;
         }
         catch( FileNotFoundException ex ) {
@@ -57,7 +57,7 @@ public class SuffixArrayReader {
             intPackedInputStream.read(occurrences);
             // Throw away the suffix array size in bytes and use the occurrences table directly.
             suffixArrayInterval = intPackedInputStream.read();
-            suffixArray = new int[occurrences[occurrences.length-1]+1/suffixArrayInterval];
+            suffixArray = new int[(occurrences[occurrences.length-1]+suffixArrayInterval-1)/suffixArrayInterval];
             intPackedInputStream.read(suffixArray);
         }
         catch( IOException ex ) {

java/src/org/broadinstitute/sting/alignment/bwa/packing/IntPackedInputStream.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.alignment.bwa.packing;
 import java.io.*;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
+import java.nio.channels.FileChannel;
 
 /**
  * Read a set of integers packed into 
@@ -14,12 +15,22 @@ public class IntPackedInputStream {
     /**
      * Ultimate target for the occurrence array.
      */
-    private final InputStream targetInputStream;
+    private final FileInputStream targetInputStream;
+
+    /**
+     * Target channel from which to pull file data.
+     */
+    private final FileChannel targetInputChannel;
 
     /**
      * The byte order in which integer input data appears.
      */
-    private final ByteBuffer buffer;
+    private final ByteOrder byteOrder;
+
+    /**
+     * How many bytes are required to store an integer?
+     */
+    private final int bytesPerInteger = PackUtils.bitsInType(Integer.class)/PackUtils.BITS_PER_BYTE;
 
     /**
      * Create a new PackedIntInputStream, writing to the given target file.
@@ -36,9 +47,10 @@ public class IntPackedInputStream {
      * @param inputStream Input stream from which to read ints.
      * @param byteOrder Endianness to use when writing a list of integers.
      */
-    public IntPackedInputStream(InputStream inputStream, ByteOrder byteOrder) {
+    public IntPackedInputStream(FileInputStream inputStream, ByteOrder byteOrder) {
         this.targetInputStream = inputStream;
-        this.buffer = ByteBuffer.allocate(PackUtils.bitsInType(Integer.class)/ PackUtils.BITS_PER_BYTE).order(byteOrder);
+        this.targetInputChannel = inputStream.getChannel();
+        this.byteOrder = byteOrder;
     }
 
     /**
@@ -69,11 +81,15 @@ public class IntPackedInputStream {
      * @throws IOException if an I/O error occurs.
      */
     public void read( int[] data, int offset, int length ) throws IOException {
-        for(int i = offset; i < offset+length; i++) {
+        ByteBuffer readBuffer = ByteBuffer.allocate(bytesPerInteger*length).order(byteOrder);
-            targetInputStream.read(buffer.array());
+
-            data[i] = buffer.getInt();
+        targetInputChannel.read(readBuffer,targetInputChannel.position());
-            buffer.rewind();
+        readBuffer.flip();
-        }
+        targetInputChannel.position(targetInputChannel.position()+readBuffer.remaining());
+
+        int i = 0;
+        while(i < length)
+            data[offset+i++] = readBuffer.getInt();
     }
 
     /**