Examples of FastqWriterFactory


    protected int doWork() {
        IOUtil.assertFileIsReadable(INPUT);
        final SAMFileReader reader = new SAMFileReader(IOUtil.openFileForReading(INPUT));
        final Map<String, SAMRecord> firstSeenMates = new HashMap<String, SAMRecord>();
        final FastqWriterFactory factory = new FastqWriterFactory();
        factory.setCreateMd5(CREATE_MD5_FILE);
        final Map<SAMReadGroupRecord, FastqWriters> writers = generateWriters(reader.getFileHeader().getReadGroups(), factory);


        final ProgressLogger progress = new ProgressLogger(log);
        for (final SAMRecord currentRecord : reader) {
            if (currentRecord.isSecondaryOrSupplementary() && !INCLUDE_NON_PRIMARY_ALIGNMENTS)

Examples of net.sf.picard.fastq.FastqWriterFactory


    private static FastqWriterFactory fastqWriterFactory;


    private static FastqWriterFactory FastqWriterFactoryInstance(){
      if(fastqWriterFactory == null){
        fastqWriterFactory = new FastqWriterFactory();
      }
      return fastqWriterFactory;
    }

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Examples of FastqWriterFactory

Examples of htsjdk.samtools.fastq.FastqWriterFactory

Examples of net.sf.picard.fastq.FastqWriterFactory