SAMBaseRecord.java Source code

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Here is the source code for SAMBaseRecord.java

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// Copyright (c) 2013 Aalto University
//
// 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.
//
// File created: 2013-02-15 10:29:29

import java.io.DataOutput;
import java.io.DataInput;
import java.io.IOException;

import org.apache.hadoop.io.Writable;

import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMRecord;

import fi.tkk.ics.hadoop.bam.SAMRecordWritable;

public class SAMBaseRecord implements Writable {
    private SAMRecordWritable parent;

    private int idx, cigarElemIdx, cigarPos;
    private CigarOperator cigarOp;
    private byte base, quality;
    private boolean noSeq, noQuals, noCigar, ownParent;

    public SAMRecordWritable getParent() {
        return parent;
    }

    public int getPos() {
        return parent.get().getAlignmentStart() + idx;
    }

    public CigarOperator getCigarOp() {
        return cigarOp;
    }

    public byte getQuality() {
        return quality;
    }

    public byte getBase() {
        return base;
    }

    public byte getCigarChar() {
        return cigarOp == null ? (byte) '*' : CigarOperator.enumToCharacter(cigarOp);
    }

    public void setParent(SAMRecordWritable wrec) {
        parent = wrec;
        ownParent = false;

        final SAMRecord rec = parent.get();

        idx = 0;

        noCigar = rec.getCigar().isEmpty();
        if (noCigar)
            cigarOp = null;
        else {
            cigarElemIdx = 0;
            cigarPos = 0;
            cigarOp = rec.getCigar().getCigarElement(0).getOperator();
        }

        gotoNextAcceptableCigarOp();
        initBaseAndQuality();
    }

    private void initBaseAndQuality() {
        final SAMRecord rec = parent.get();

        final byte[] bases = rec.getReadBases();
        noSeq = bases == SAMRecord.NULL_SEQUENCE;
        base = noSeq ? -1 : bases[idx];

        final byte[] quals = rec.getBaseQualities();
        noQuals = quals == SAMRecord.NULL_QUALS;
        quality = noQuals ? -1 : quals[idx];
    }

    public boolean gotoNextBase() {
        final SAMRecord rec = parent.get();

        if (++idx == rec.getReadLength())
            return false;

        if (!noSeq)
            base = rec.getReadBases()[idx];
        if (!noQuals)
            quality = rec.getBaseQualities()[idx];

        if (!noCigar) {
            final Cigar cigar = rec.getCigar();
            final CigarElement cigarElem = cigar.getCigarElement(cigarElemIdx);

            ++cigarPos;
            if (cigarPos == cigarElem.getLength()) {
                ++cigarElemIdx;
                cigarOp = cigar.getCigarElement(cigarElemIdx).getOperator();
                cigarPos = 0;
                gotoNextAcceptableCigarOp();
            }
        }
        return true;
    }

    private void gotoNextAcceptableCigarOp() {
        assert !noCigar;

        // This shouldn't run off the end of the array since idx hasn't reached
        // getReadLength() yet.
        final Cigar cigar = parent.get().getCigar();
        while (!cigarOp.consumesReadBases())
            cigarOp = cigar.getCigarElement(++cigarElemIdx).getOperator();
    }

    @Override
    public void write(DataOutput out) throws IOException {
        parent.write(out);
        out.writeInt(idx);
        if (!noCigar) {
            out.writeInt(cigarElemIdx);
            out.writeInt(cigarPos);
        }
    }

    @Override
    public void readFields(DataInput in) throws IOException {
        if (parent == null || !ownParent) {
            parent = new SAMRecordWritable();
            ownParent = true;
        }
        parent.readFields(in);
        idx = in.readInt();

        final SAMRecord rec = parent.get();

        noCigar = rec.getCigar().isEmpty();
        if (noCigar)
            cigarOp = null;
        else {
            cigarElemIdx = in.readInt();
            cigarPos = in.readInt();
            cigarOp = rec.getCigar().getCigarElement(cigarElemIdx).getOperator();
        }

        initBaseAndQuality();
    }
}