95 lines
2.8 KiB
Java
95 lines
2.8 KiB
Java
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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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*
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* @author aaron
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*
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* Class SinglePointCall
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*
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* This class represents a single point geneotype call in GLF vernacular
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**/
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class SinglePointCall extends GLFRecord {
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// our likelyhood array size
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public static final int LIKELYHOOD_SIZE = 10;
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// our record type
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private final RECORD_TYPE type = RECORD_TYPE.SINGLE;
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// our array of likelihoods
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public final short lk[] = new short[LIKELYHOOD_SIZE];
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// our size, we're immutable (the size at least). In bytes.
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private final int byteSize;
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SinglePointCall(char refBase, int offset, int readDepth, short rmsMapQ, short[] lk, LikelihoodObject minimumLikelihood ) {
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super(refBase,offset,(short)minimumLikelihood.getMinimumValue(),readDepth,rmsMapQ);
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if (lk.length != LIKELYHOOD_SIZE) {
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throw new IllegalArgumentException("SinglePointCall: passed in likelyhood array size != LIKELYHOOD_SIZE");
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}
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System.arraycopy(lk, 0, this.lk, 0, LIKELYHOOD_SIZE);
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byteSize = 9 + lk.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
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*/
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public void write( BinaryCodec out ) {
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super.write(out);
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for (int x = 0; x < LIKELYHOOD_SIZE; x++) {
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out.writeUByte(lk[x]);
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}
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}
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/**
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* return the record type we represent, in this case SINGLE
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* @return RECORD_TYPE.SINGLE
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*/
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public RECORD_TYPE getRecordType() {
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return RECORD_TYPE.SINGLE;
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}
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/**
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* return our size in bytes
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* @return number of bytes we represent
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*/
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public int getByteSize() {
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return byteSize;
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}
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}
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