Examples with PicardException picard.PicardException used on opensource projects

Example 1 with PicardException

use of picard.PicardException in project gridss by PapenfussLab.

the class ByReadNameSinglePassSamProgram method makeItSo.

public static void makeItSo(final File input, final File referenceSequence, final boolean assumeSorted, final long stopAfter, final Collection<ByReadNameSinglePassSamProgram> programs) throws FileNotFoundException {
    // Setup the standard inputs
    IOUtil.assertFileIsReadable(input);
    SamReader in = SamReaderFactory.makeDefault().referenceSequence(referenceSequence).open(input);
    // Optionally load up the reference sequence and double check sequence dictionaries
    final ReferenceLookup lookup;
    if (referenceSequence == null) {
        lookup = null;
    } else {
        IOUtil.assertFileIsReadable(referenceSequence);
        lookup = new TwoBitBufferedReferenceSequenceFile(new IndexedFastaSequenceFile(referenceSequence));
        if (!in.getFileHeader().getSequenceDictionary().isEmpty()) {
            SequenceUtil.assertSequenceDictionariesEqual(in.getFileHeader().getSequenceDictionary(), lookup.getSequenceDictionary());
        }
    }
    // Check on the sort order of the BAM file
    final SortOrder sort = in.getFileHeader().getSortOrder();
    if (sort != SortOrder.queryname) {
        if (assumeSorted) {
            log.warn("File reports sort order '" + sort + "', assuming it's queryname sorted anyway.");
        } else {
            throw new PicardException("File " + input.getAbsolutePath() + " should be queryname sorted but " + "the header says the sort order is " + sort + ". If you believe the file " + "to be queryname sorted you may pass ASSUME_SORTED=true");
        }
    }
    for (final ByReadNameSinglePassSamProgram program : programs) {
        program.setReference(lookup);
        program.setup(in.getFileHeader(), input);
    }
    final ProgressLogger progress = new ProgressLogger(log);
    final SAMRecordIterator rawit = in.iterator();
    final CloseableIterator<SAMRecord> it = new AsyncBufferedIterator<SAMRecord>(rawit, "ByReadNameSinglePassSamProgram " + input.getName());
    try {
        List<SAMRecord> currentRecords = new ArrayList<>();
        String currentReadName = null;
        while (it.hasNext()) {
            SAMRecord r = it.next();
            String readname = r.getReadName();
            // if read name we have to just treat it as a single read
            if (readname == null || !readname.equals(currentReadName)) {
                if (currentRecords.size() > 0) {
                    for (final ByReadNameSinglePassSamProgram program : programs) {
                        program.acceptFragment(currentRecords, lookup);
                    }
                }
                currentRecords.clear();
                currentReadName = readname;
                if (stopAfter > 0 && progress.getCount() >= stopAfter) {
                    break;
                }
            }
            currentRecords.add(r);
            progress.record(r);
        }
        if (currentRecords.size() > 0) {
            for (final ByReadNameSinglePassSamProgram program : programs) {
                program.acceptFragment(currentRecords, lookup);
            }
        }
    } finally {
        CloserUtil.close(it);
        CloserUtil.close(rawit);
        CloserUtil.close(in);
    }
    for (final ByReadNameSinglePassSamProgram program : programs) {
        program.finish();
    }
}