Small standalone utility to aggregate BGZF block statistics in a BAM file.

Works in the same coordinate space as BAM chunks, so this will be used to
calibrate chunk weighting.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5531 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java

@@ -0,0 +1,137 @@
+/*
+ * Copyright (c) 2011, 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.gatk.datasources.reads.utilities;
+
+import net.sf.samtools.SAMFileReader;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
+
+/**
+ * Calculates the bounds of each BGZF block in a BAM index file, along with
+ */
+public class PrintBGZFBounds extends CommandLineProgram {
+    @Argument(fullName="input",shortName="I",doc="Input bai file to process",required=true)
+    private File input = null;
+
+    private final int BYTE_SIZE_IN_BYTES = Byte.SIZE / 8;
+    private final int INT_SIZE_IN_BYTES = Integer.SIZE / 8;
+    private final int SHORT_SIZE_IN_BYTES = INT_SIZE_IN_BYTES / 2;
+
+    /**
+     * ID1 + ID2 + CM + FLG + MTIME + XFL + OS + XLEN.
+     */
+    private final int HEADER_SIZE = BYTE_SIZE_IN_BYTES*4+INT_SIZE_IN_BYTES+BYTE_SIZE_IN_BYTES*2+SHORT_SIZE_IN_BYTES + BYTE_SIZE_IN_BYTES*2 + SHORT_SIZE_IN_BYTES*2;;
+
+    /**
+     * CRC32 + ISIZE
+     */
+    private final int FOOTER_SIZE = INT_SIZE_IN_BYTES*2;
+
+    @Override
+    public int execute() throws IOException {
+        FileInputStream fis = new FileInputStream(input);
+        ByteBuffer headerBuffer = allocateBuffer(HEADER_SIZE);
+        ByteBuffer footerBuffer = allocateBuffer(FOOTER_SIZE);
+
+        float compressedSize = 0;
+        float uncompressedSize = 0;
+        long totalBlocks = 0;
+
+        //SAMFileReader reader = new SAMFileReader(input);
+
+        while(true) {
+            final long blockStart = fis.getChannel().position();
+
+            int totalRead = fis.getChannel().read(headerBuffer);
+            if(totalRead <= 0)
+                break;
+            headerBuffer.flip();
+
+            // Read out header information, including subfield IDs.
+            headerBuffer.position(headerBuffer.capacity()-BYTE_SIZE_IN_BYTES*2);
+            final int cDataSize = headerBuffer.getShort()-HEADER_SIZE-FOOTER_SIZE+1;
+            compressedSize += cDataSize;
+
+            // Skip past body.
+            fis.getChannel().position(fis.getChannel().position()+cDataSize);
+
+            // Read the footer
+            fis.getChannel().read(footerBuffer);
+            footerBuffer.flip();
+
+            // Retrieve the uncompressed size from the footer.
+            footerBuffer.position(footerBuffer.capacity()-INT_SIZE_IN_BYTES);
+            uncompressedSize += footerBuffer.getInt();
+
+            // Reset buffers for subsequent reads.
+            headerBuffer.flip();
+            footerBuffer.flip();
+
+            totalBlocks++;
+
+            final long blockStop = fis.getChannel().position() - 1;
+
+            System.out.printf("BGZF block %d: [%d-%d]%n",totalBlocks,blockStart,blockStop);
+        }
+
+        System.out.printf("SUCCESS!  Average compressed block size = %f, average uncompressed size = %f, compressed/uncompressed ratio: %f%n",compressedSize/totalBlocks,uncompressedSize/totalBlocks,compressedSize/uncompressedSize);
+
+        return 0;
+    }
+
+    private ByteBuffer allocateBuffer(final int size) {
+        ByteBuffer buffer = ByteBuffer.allocate(size);
+        buffer.order(ByteOrder.LITTLE_ENDIAN);
+        return buffer;
+    }
+
+    /**
+     * Required main method implementation.
+     * @param argv Command-line argument text.
+     * @throws Exception on error.
+     */
+    public static void main(String[] argv) throws Exception {
+        int returnCode = 0;
+        try {
+            PrintBGZFBounds instance = new PrintBGZFBounds();
+            start(instance, argv);
+            returnCode = 0;
+        }
+        catch(Exception ex) {
+            returnCode = 1;
+            ex.printStackTrace();
+            throw ex;
+        }
+        finally {
+            System.exit(returnCode);
+        }
+    }
+}