126 lines
4.6 KiB
Java
126 lines
4.6 KiB
Java
/*
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* Copyright (c) 2010 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.datasources;
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import org.broadinstitute.sting.commandline.CommandLineProgram;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.utils.StingException;
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import java.io.File;
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import java.io.PrintStream;
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import net.sf.samtools.*;
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/**
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*
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*
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* @author mhanna
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* @version 0.1
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*/
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public class BAMFileStat extends CommandLineProgram {
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public enum CommandType { ShowBlocks, ShowIndex }
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@Argument(doc="Which operation to run.",required=true)
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private CommandType command;
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@Argument(doc="The BAM file to inspect.",required=true)
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private String bamFileName;
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@Argument(doc="The range of blocks to inspect.",required=false)
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private String range;
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public int execute() {
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Integer startPosition = null, stopPosition = null;
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if(range != null) {
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int dashPosition = range.indexOf('-');
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if(dashPosition > 0) {
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if(dashPosition > 0)
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startPosition = Integer.valueOf(range.substring(0,dashPosition));
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if(dashPosition < range.length()-1)
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stopPosition = Integer.valueOf(range.substring(dashPosition+1));
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}
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else
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startPosition = Integer.valueOf(range);
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}
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switch(command) {
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case ShowBlocks:
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throw new StingException("The BAM block inspector has been disabled.");
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case ShowIndex:
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showIndexBins(new File(bamFileName+".bai"));
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break;
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}
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return 0;
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}
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/**
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* Required main method implementation.
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* @param argv Command-line arguments.
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*/
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public static void main(String[] argv) {
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try {
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BAMFileStat instance = new BAMFileStat();
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start(instance, argv);
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System.exit(CommandLineProgram.result);
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} catch (Exception e) {
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exitSystemWithError(e);
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}
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}
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private void showIndexBins(File bamFile) {
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BAMFileIndexContentInspector inspector = new BAMFileIndexContentInspector(bamFile);
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inspector.inspect(System.out,null,null);
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}
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private class BAMFileIndexContentInspector /*extends CachingBAMFileIndex*/ {
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public BAMFileIndexContentInspector(File bamFileIndex) {
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// super(bamFileIndex);
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}
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public void inspect(PrintStream outputStream, Integer startPosition, Integer stopPosition) {
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/*
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outputStream.printf("Number of reference sequences: %d%n", this.referenceToBins.size());
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for(int referenceSequence: referenceToBins.keySet()) {
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Bin[] bins = referenceToBins.get(referenceSequence);
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outputStream.printf("Reference sequence: %d%n",referenceSequence);
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outputStream.printf("number of bins: %d%n",bins.length);
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for(Bin bin: bins) {
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List<Chunk> chunks = binToChunks.get(bin);
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outputStream.printf("\tBin: %d, number of chunks: %d%n", bin.binNumber, chunks.size());
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for(Chunk chunk: chunks)
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outputStream.printf("\t\tChunk: %s%n", chunk);
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}
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LinearIndex linearIndex = referenceToLinearIndices.get(referenceSequence);
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outputStream.printf("\t\tIndex entries: %d", linearIndex.indexEntries.length);
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for(long indexEntry: linearIndex.indexEntries)
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outputStream.printf("%d,",indexEntry);
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outputStream.printf("%n");
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}
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*/
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}
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}
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}
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