65 lines
2.2 KiB
Java
65 lines
2.2 KiB
Java
/*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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package edu.mit.broad.sam;
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import edu.mit.broad.sam.util.BinaryCodec;
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import edu.mit.broad.sam.util.BlockCompressedOutputStream;
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import java.io.DataOutputStream;
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import java.io.File;
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/**
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* Concrete implementation of SAMFileWriter for writing gzipped BAM files.
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*/
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class BAMFileWriter extends SAMFileWriterImpl {
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private final BinaryCodec outputBinaryCodec;
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private BAMRecordCodec bamRecordCodec = null;
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public BAMFileWriter(final File path) {
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outputBinaryCodec = new BinaryCodec(new DataOutputStream(new BlockCompressedOutputStream(path)));
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outputBinaryCodec.setOutputFileName(path.toString());
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}
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private void prepareToWriteAlignments() {
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if (bamRecordCodec == null) {
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bamRecordCodec = new BAMRecordCodec(getHeader());
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bamRecordCodec.setOutputStream(outputBinaryCodec.getOutputStream());
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}
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}
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protected void writeAlignment(final SAMRecord alignment) {
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prepareToWriteAlignments();
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bamRecordCodec.encode(alignment);
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}
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protected void writeHeader(final String textHeader) {
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outputBinaryCodec.writeBytes(BAMFileConstants.BAM_MAGIC);
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// calculate and write the length of the SAM file header text and the header text
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outputBinaryCodec.writeString(textHeader, true, false);
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// write the sequences binarily. This is redundant with the text header
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outputBinaryCodec.writeInt(getHeader().getSequences().size());
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for (final SAMSequenceRecord sequenceRecord: getHeader().getSequences()) {
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outputBinaryCodec.writeString(sequenceRecord.getSequenceName(), true, true);
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outputBinaryCodec.writeInt(sequenceRecord.getSequenceLength());
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}
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}
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protected void finish() {
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outputBinaryCodec.close();
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}
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protected String getFilename() {
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return outputBinaryCodec.getOutputFileName();
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}
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}
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