Examples of SAMFileWriterStub

org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub
A stub for routing and management of SAM file reading and writing. @author mhanna @version 0.1

Examples of org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub

     * @param file the filename to write to
     * @param engine the engine
     * @return a SAMFileWriter with the correct options set
     */
    public static SAMFileWriter createSAMFileWriter(final String file, final GenomeAnalysisEngine engine) {
        final SAMFileWriterStub output = new SAMFileWriterStub(engine, new File(file));
        output.processArguments(engine.getArguments());
        return output;
    }

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Examples of org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub


    /**
     *  As {@link #createSAMFileWriter(String, org.broadinstitute.gatk.engine.GenomeAnalysisEngine)}, but also sets the header
     */
    public static SAMFileWriter createSAMFileWriter(final String file, final GenomeAnalysisEngine engine, final SAMFileHeader header) {
        final SAMFileWriterStub output = (SAMFileWriterStub) createSAMFileWriter(file, engine);
        output.writeHeader(header);
        return output;
    }

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