/*
 * Copyright (c) 2010 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.alignment;

import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.alignment.bwa.BWTFiles;
import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import net.sf.samtools.SAMRecord;

import java.util.*;
import java.io.PrintStream;

/**
 * Counts the number of best alignments as presented by BWA and outputs a histogram of number of placements vs. the
 * frequency of that number of placements.
 *
 * @author mhanna
 * @version 0.1
 */
public class CountBestAlignmentsWalker extends ReadWalker<Integer,Integer> {
    /**
     * The supporting BWT index generated using BWT.
     */
    @Argument(fullName="BWTPrefix",shortName="BWT",doc="Index files generated by bwa index -d bwtsw",required=false)
    private String prefix = null;

    @Output
    private PrintStream out = null;    

    /**
     * The actual aligner.
     */
    private Aligner aligner = null;

    private SortedMap<Integer,Integer> alignmentFrequencies = new TreeMap<Integer,Integer>();

    /**
     * Create an aligner object.  The aligner object will load and hold the BWT until close() is called.
     */
    @Override
    public void initialize() {
        if(prefix == null)
            prefix = getToolkit().getArguments().referenceFile.getAbsolutePath();        
        BWTFiles bwtFiles = new BWTFiles(prefix);
        BWAConfiguration configuration = new BWAConfiguration();
        aligner = new BWACAligner(bwtFiles,configuration);
    }

    /**
     * Aligns a read to the given reference.
     * @param ref Reference over the read.  Read will most likely be unmapped, so ref will be null.
     * @param read Read to align.
     * @return Number of alignments found for this read.
     */
    @Override
    public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
        Iterator<Alignment[]> alignmentIterator = aligner.getAllAlignments(read.getReadBases()).iterator();
        if(alignmentIterator.hasNext()) {
            int numAlignments = alignmentIterator.next().length;
            if(alignmentFrequencies.containsKey(numAlignments))
                alignmentFrequencies.put(numAlignments,alignmentFrequencies.get(numAlignments)+1);
            else
                alignmentFrequencies.put(numAlignments,1);
        }
        return 1;
    }    

    /**
     * Initial value for reduce.  In this case, validated reads will be counted.
     * @return 0, indicating no reads yet validated.
     */
    @Override
    public Integer reduceInit() { return 0; }

    /**
     * Calculates the number of reads processed.
     * @param value Number of reads processed by this map.
     * @param sum Number of reads processed before this map.
     * @return Number of reads processed up to and including this map.
     */
    @Override
    public Integer reduce(Integer value, Integer sum) {
        return value + sum;
    }

    /**
     * Cleanup.
     * @param result Number of reads processed.
     */
    @Override
    public void onTraversalDone(Integer result) {
        aligner.close();
        for(Map.Entry<Integer,Integer> alignmentFrequency: alignmentFrequencies.entrySet())
            out.printf("%d\t%d%n", alignmentFrequency.getKey(), alignmentFrequency.getValue());
        super.onTraversalDone(result);
    }
}
