org.ncic.bioinfo.sparkseq.algorithms.data.sam.IntervalLocusSamTraverser.java Source code

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Here is the source code for org.ncic.bioinfo.sparkseq.algorithms.data.sam.IntervalLocusSamTraverser.java

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/*
 * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences
 *
 * 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.ncic.bioinfo.sparkseq.algorithms.data.sam;

import org.apache.commons.collections.CollectionUtils;
import org.ncic.bioinfo.sparkseq.algorithms.data.sam.filter.FilterUtils;
import org.ncic.bioinfo.sparkseq.algorithms.utils.GenomeLoc;
import org.ncic.bioinfo.sparkseq.exceptions.GATKException;

import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.stream.Collectors;

/**
 * Author: wbc
 */
public class IntervalLocusSamTraverser {

    private static final int OVERLAP_LEN = 100;
    private final List<GenomeLoc> intervals;
    private final LocusSamTraverser locusSamTraverser;

    public IntervalLocusSamTraverser(SamContentProvider samContentProvider, GenomeLoc refLocus,
            List<GenomeLoc> rawTraverseIntervals) {
        this(samContentProvider, refLocus, rawTraverseIntervals, new FilterUtils());
    }

    public IntervalLocusSamTraverser(SamContentProvider samContentProvider, GenomeLoc refLocus,
            List<GenomeLoc> rawTraverseIntervals, FilterUtils filterUtils) {
        this.intervals = getOverlappedIntervals(refLocus, rawTraverseIntervals);
        this.locusSamTraverser = new LocusSamTraverser(samContentProvider, refLocus, filterUtils);
        rewind();
    }

    private List<GenomeLoc> getOverlappedIntervals(GenomeLoc refLocus, List<GenomeLoc> rawTraverseIntervals) {
        // intervalsrefLocus??
        if (CollectionUtils.isEmpty(rawTraverseIntervals)) {
            List<GenomeLoc> singleGenomeLoc = new ArrayList<>(1);
            singleGenomeLoc.add(refLocus);
            return singleGenomeLoc;
        }

        List<GenomeLoc> rawOverlappedIntervals = rawTraverseIntervals.stream()
                .filter(interval -> interval.overlapsP(refLocus))
                .map(interval -> new GenomeLoc(interval.getContig(), interval.getContigIndex(),
                        (interval.getStart() - OVERLAP_LEN) < refLocus.getStart() ? refLocus.getStart()
                                : (interval.getStart() - OVERLAP_LEN),
                        (interval.getStop() + OVERLAP_LEN) > refLocus.getStop() ? refLocus.getStop()
                                : (interval.getStop() + OVERLAP_LEN)))
                .collect(Collectors.toList());

        Collections.sort(rawOverlappedIntervals,
                (interval1, interval2) -> interval1.getStart() - interval2.getStart());

        //?intervals
        List<GenomeLoc> finalIntervals = new ArrayList<>();
        GenomeLoc tmpInterval = null;
        for (GenomeLoc interval : rawOverlappedIntervals) {
            if (tmpInterval == null) {
                tmpInterval = interval;
            } else {
                if (tmpInterval.overlapsP(interval)) {
                    tmpInterval = new GenomeLoc(tmpInterval.getContig(), tmpInterval.getContigIndex(),
                            Integer.min(tmpInterval.getStart(), interval.getStart()),
                            Integer.max(tmpInterval.getStop(), interval.getStop()));
                } else {
                    finalIntervals.add(tmpInterval);
                    tmpInterval = interval;
                }
            }
        }
        if (tmpInterval != null) {
            finalIntervals.add(tmpInterval);
        }

        return finalIntervals;
    }

    private int curIntervalIdx = -1;
    private int curCoordinate = -1;

    public void rewind() {
        curIntervalIdx = 0;
        curCoordinate = intervals.get(curIntervalIdx).getStart();
    }

    public boolean hasNext() {
        return curIntervalIdx < intervals.size() - 1 || (curIntervalIdx == intervals.size() - 1
                && curCoordinate <= intervals.get(intervals.size() - 1).getStop());
    }

    public AlignmentContext next() {
        if (!hasNext()) {
            throw new GATKException("Out of bound when traverse sam content provider");
        }

        locusSamTraverser.forwardToCoordinate(curCoordinate);
        AlignmentContext alignmentContext = locusSamTraverser.next();

        // curCoordinate
        if (curCoordinate == intervals.get(curIntervalIdx).getStop()) {
            curIntervalIdx++;
            if (curIntervalIdx < intervals.size()) { // intervalcoordinate
                curCoordinate = intervals.get(curIntervalIdx).getStart();
            }
        } else {
            curCoordinate++;
        }

        return alignmentContext;
    }
}