Examples with NDNCigarReadTransformer org.broadinstitute.hellbender.transformers.NDNCigarReadTransformer used on opensource projects

Example 1 with NDNCigarReadTransformer

use of org.broadinstitute.hellbender.transformers.NDNCigarReadTransformer in project gatk by broadinstitute.

the class SplitNCigarReads method onTraversalStart.

@Override
public void onTraversalStart() {
    header = getHeaderForSAMWriter();
    rnaReadTransform = REFACTOR_NDN_CIGAR_READS ? new NDNCigarReadTransformer() : ReadTransformer.identity();
    try {
        referenceReader = new CachingIndexedFastaSequenceFile(referenceArguments.getReferenceFile());
        GenomeLocParser genomeLocParser = new GenomeLocParser(getBestAvailableSequenceDictionary());
        outputWriter = createSAMWriter(OUTPUT, false);
        overhangManager = new OverhangFixingManager(header, outputWriter, genomeLocParser, referenceReader, MAX_RECORDS_IN_MEMORY, MAX_MISMATCHES_IN_OVERHANG, MAX_BASES_TO_CLIP, doNotFixOverhangs, processSecondaryAlignments);
    } catch (FileNotFoundException ex) {
        throw new UserException.CouldNotReadInputFile(referenceArguments.getReferenceFile(), ex);
    }
}