124 lines
4.7 KiB
Java
124 lines
4.7 KiB
Java
package org.broadinstitute.sting.utils.glf;
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import net.sf.samtools.util.BinaryCodec;
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/*
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* Copyright (c) 2009 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 THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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/**
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* @author aaron
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* <p/>
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* Class VariableLengthCall
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* <p/>
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* This class represents variable length genotype calls in the GLF format.
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* Currently a lot of parameters need to be provided, but we may be able to thin
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* those down as we understand what we have to specify and what we can infer.
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*/
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class VariableLengthCall extends GLFRecord {
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// our fields, corresponding to the glf spec
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private short lkHom1 = 0;
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private short lkHom2 = 0;
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private short lkHet = 0;
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private int indelLen1 = 0;
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private int indelLen2 = 0;
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private final short indelSeq1[];
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private final short indelSeq2[];
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// our size, which is immutable, in bytes
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private final int size;
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/**
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* the default constructor
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*
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* @param refBase the reference base
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* @param offset the location, as an offset from the previous glf record
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* @param readDepth the read depth at the specified postion
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* @param rmsMapQ the root mean square of the mapping quality
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* @param minimumLikelihood the minimum likelihood value
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* @param lkHom1 the negitive log likelihood of the first homozygous indel allele, from 0 to 255
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* @param lkHom2 the negitive log likelihood of the second homozygous indel allele, from 0 to 255
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* @param lkHet the negitive log likelihood of the heterozygote, from 0 to 255
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* @param indelLen1 the length of the first indel allele
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* @param indelLen2 the length of the second indel allele
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* @param indelSeq1 the sequence for the first indel allele
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* @param indelSeq2 the sequence for the second indel allele
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*/
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VariableLengthCall( char refBase,
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long offset,
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int readDepth,
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short minimumLikelihood,
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short rmsMapQ,
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short lkHom1,
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short lkHom2,
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short lkHet,
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int indelLen1,
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int indelLen2,
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final short indelSeq1[],
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final short indelSeq2[] ) {
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super(refBase, offset, minimumLikelihood, readDepth, rmsMapQ);
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this.lkHom1 = lkHom1;
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this.lkHom2 = lkHom2;
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this.lkHet = lkHet;
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this.indelLen1 = indelLen1;
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this.indelLen2 = indelLen2;
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this.indelSeq1 = indelSeq1;
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this.indelSeq2 = indelSeq2;
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size = 16 + indelSeq1.length + indelSeq2.length;
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}
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/**
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* Write out the record to a binary codec
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*
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* @param out the binary codec to write to
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*/
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void write( BinaryCodec out ) {
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super.write(out);
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out.writeByte(lkHom1);
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out.writeByte(lkHom2);
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out.writeByte(lkHet);
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out.writeShort(new Integer(indelLen1).shortValue());
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out.writeShort(new Integer(indelLen2).shortValue());
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for (int x = 0; x < indelSeq1.length; x++) {
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out.writeUByte(indelSeq1[x]);
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}
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for (int x = 0; x < indelSeq2.length; x++) {
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out.writeUByte(indelSeq2[x]);
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}
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}
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/** @return RECORD_TYPE.VARIABLE */
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public RECORD_TYPE getRecordType() {
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return RECORD_TYPE.VARIABLE;
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}
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/** @return the size of the record, which is the size of our fields plus the generic records fields */
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public int getByteSize() {
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return size + super.getByteSize();
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}
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}
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