Examples with ReaderSplitter org.broadinstitute.hellbender.tools.readersplitters.ReaderSplitter used on opensource projects

Example 1 with ReaderSplitter

use of org.broadinstitute.hellbender.tools.readersplitters.ReaderSplitter in project gatk by broadinstitute.

the class SplitReads method createWriters.

/**
     * Creates SAMFileWriter instances for the reader splitters based on the input file.
     * @param splitters Reader splitters.
     * @return A map of file name keys to SAMFileWriter.
     */
private Map<String, SAMFileGATKReadWriter> createWriters(final List<ReaderSplitter<?>> splitters) {
    final Map<String, SAMFileGATKReadWriter> outs = new LinkedHashMap<>();
    final SAMFileWriterFactory samFileWriterFactory = new SAMFileWriterFactory();
    final SAMFileHeader samFileHeaderIn = getHeaderForReads();
    // Build up a list of key options at each level.
    final List<List<?>> splitKeys = splitters.stream().map(splitter -> splitter.getSplitsBy(samFileHeaderIn)).collect(Collectors.toList());
    // For every combination of keys, add a SAMFileWriter.
    addKey(splitKeys, 0, "", key -> {
        outs.put(key, prepareSAMFileWriter(samFileWriterFactory, samFileHeaderIn, key));
    });
    return outs;
}