77 lines
2.1 KiB
Java
77 lines
2.1 KiB
Java
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package org.broadinstitute.sting.utils.sam;
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import net.sf.samtools.SAMFileWriter;
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import net.sf.samtools.SAMRecord;
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import java.util.ArrayList;
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import java.util.List;
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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 ArtificialSAMFileWriter
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* <p/>
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* generates a fike samwriter, that you can get the output reads
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* from when you're done.
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*/
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public class ArtificialSAMFileWriter implements SAMFileWriter {
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// are we closed
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private boolean closed = false;
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// the SAMRecords we've added to this writer
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List<SAMRecord> records = new ArrayList<SAMRecord>();
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public void addAlignment( SAMRecord alignment ) {
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records.add(alignment);
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}
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/** not much to do when we're fake */
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public void close() {
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closed = true;
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}
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/**
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* are we closed?
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*
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* @return true if we're closed
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*/
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public boolean isClosed() {
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return closed;
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}
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/**
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* get the records we've seen
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* @return
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*/
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public List<SAMRecord> getRecords() {
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return records;
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}
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}
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