Examples with SAMFileGATKReadWriter org.broadinstitute.hellbender.utils.read.SAMFileGATKReadWriter used on opensource projects

Example 1 with SAMFileGATKReadWriter

use of org.broadinstitute.hellbender.utils.read.SAMFileGATKReadWriter 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;
}

Example 2 with SAMFileGATKReadWriter

use of org.broadinstitute.hellbender.utils.read.SAMFileGATKReadWriter in project gatk by broadinstitute.

the class ReadsDataSourceUnitTest method getFileWithAddedContig.

// Copy the reads in the inputFile to the output file, adding an extra contig to the sequence dictionary
// and a read referencing that contig
private File getFileWithAddedContig(final Path inputPath, final String extraContig, final String outputName, final String extension) {
    final File outputFile = BaseTest.createTempFile(outputName, extension);
    try (ReadsDataSource readsSource = new ReadsDataSource(inputPath)) {
        SAMFileHeader header = readsSource.getHeader();
        SAMSequenceRecord fakeSequenceRec = new SAMSequenceRecord(extraContig, 100);
        header.addSequence(fakeSequenceRec);
        try (final SAMFileGATKReadWriter gatkReadWriter = new SAMFileGATKReadWriter(ReadUtils.createCommonSAMWriter(outputFile, null, header, true, true, false))) {
            for (final GATKRead read : readsSource) {
                gatkReadWriter.addRead(read);
            }
            // use the contig name in the read name to make it easy to see where this read came from
            SAMRecord samRec = new SAMRecord(header);
            samRec.setReadName(extraContig + "_READ");
            samRec.setReferenceName(extraContig);
            samRec.setAlignmentStart(5);
            samRec.setReadBases(new byte[] { 'a', 'c', 'g', 't' });
            gatkReadWriter.addRead(new SAMRecordToGATKReadAdapter(samRec));
        }
    }
    return outputFile;
}