Examples with SAMRecordIterator htsjdk.samtools.SAMRecordIterator used on opensource projects

Example 66 with SAMRecordIterator

use of htsjdk.samtools.SAMRecordIterator in project gridss by PapenfussLab.

the class SAMEvidenceSource method iterator.

public CloseableIterator<DirectedEvidence> iterator(final QueryInterval[] intervals) {
    SamReader reader = getReader();
    // expand query bounds as the alignment for a discordant read pair could fall before or after the breakend interval we are extracting
    SAMRecordIterator it = tryOpenReader(reader, QueryIntervalUtil.padIntervals(getContext().getDictionary(), intervals, getMaxConcordantFragmentSize() + 1));
    Iterator<DirectedEvidence> eit = asEvidence(it);
    eit = Iterators.filter(eit, e -> QueryIntervalUtil.overlaps(intervals, e.getBreakendSummary()));
    return new AutoClosingIterator<>(eit, reader, it);
}

Example 67 with SAMRecordIterator

use of htsjdk.samtools.SAMRecordIterator in project gridss by PapenfussLab.

the class SAMEvidenceSource method iterator.

public CloseableIterator<DirectedEvidence> iterator() {
    SamReader reader = getReader();
    SAMRecordIterator it = reader.iterator();
    it.assertSorted(SortOrder.coordinate);
    Iterator<DirectedEvidence> eit = asEvidence(it);
    return new AutoClosingIterator<>(eit, reader, it);
}

Example 68 with SAMRecordIterator

use of htsjdk.samtools.SAMRecordIterator in project gridss by PapenfussLab.

the class ExternalProcessFastqAligner method align.

@Override
public void align(final File fastq, final File output, final File reference, final int threads) throws IOException {
    List<String> commandline = template.stream().map(s -> String.format(s, fastq.getAbsolutePath(), reference.getAbsolutePath(), threads)).collect(Collectors.toList());
    String commandlinestr = commandline.stream().collect(Collectors.joining(" "));
    log.info("Invoking external aligner");
    log.info(commandlinestr);
    Process aligner = new ProcessBuilder(commandline).redirectError(Redirect.INHERIT).directory(output.getParentFile()).start();
    final SamReader reader = readerFactory.open(SamInputResource.of(aligner.getInputStream()));
    final SAMFileHeader header = reader.getFileHeader();
    try (final SAMFileWriter writer = writerFactory.makeWriter(header, false, output, reference)) {
        final SAMRecordIterator it = reader.iterator();
        while (it.hasNext()) {
            writer.addAlignment(it.next());
        }
    }
    ExternalProcessHelper.shutdownAligner(aligner, commandlinestr, reference);
}

Example 69 with SAMRecordIterator

use of htsjdk.samtools.SAMRecordIterator in project gridss by PapenfussLab.

the class ExternalProcessStreamingAligner method readAllAlignments.

private void readAllAlignments(final SamReaderFactory readerFactory) {
    SamReader fromExternalProgram = readerFactory.open(SamInputResource.of(aligner.getInputStream()));
    SAMRecordIterator it = fromExternalProgram.iterator();
    while (it.hasNext()) {
        SAMRecord r = it.next();
        buffer.add(r);
        outstandingReads.decrementAndGet();
    }
    log.info("Reader thread complete.");
}

Example 70 with SAMRecordIterator

use of htsjdk.samtools.SAMRecordIterator in project jvarkit by lindenb.

the class PcrClipReads method run.

private int run(final SamReader reader) {
    final SAMFileHeader header1 = reader.getFileHeader();
    final SAMFileHeader header2 = header1.clone();
    Optional<SAMProgramRecord> samProgramRecord = Optional.empty();
    if (this.programId) {
        final SAMProgramRecord spr = header2.createProgramRecord();
        samProgramRecord = Optional.of(spr);
        spr.setProgramName(PcrClipReads.class.getSimpleName());
        spr.setProgramVersion(this.getGitHash());
        spr.setCommandLine(getProgramCommandLine().replace('\t', ' '));
    }
    header2.addComment(getProgramName() + " " + getVersion() + ": Processed with " + getProgramCommandLine());
    header2.setSortOrder(SortOrder.unsorted);
    SAMFileWriter sw = null;
    SAMRecordIterator iter = null;
    try {
        sw = this.writingBamArgs.openSAMFileWriter(outputFile, header2, false);
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header1).logger(LOG);
        iter = reader.iterator();
        while (iter.hasNext()) {
            SAMRecord rec = progress.watch(iter.next());
            if (this.onlyFlag != -1 && (rec.getFlags() & this.onlyFlag) != 0) {
                sw.addAlignment(rec);
                continue;
            }
            if (rec.getReadUnmappedFlag()) {
                sw.addAlignment(rec);
                continue;
            }
            final Interval fragment = findInterval(rec);
            if (fragment == null) {
                rec.setMappingQuality(0);
                sw.addAlignment(rec);
                continue;
            }
            // strand is '-' and overap in 5' of PCR fragment
            if (rec.getReadNegativeStrandFlag() && fragment.getStart() < rec.getAlignmentStart() && rec.getAlignmentStart() < fragment.getEnd()) {
                rec.setMappingQuality(0);
                sw.addAlignment(rec);
                continue;
            }
            // strand is '+' and overap in 3' of PCR fragment
            if (!rec.getReadNegativeStrandFlag() && fragment.getStart() < rec.getAlignmentEnd() && rec.getAlignmentEnd() < fragment.getEnd()) {
                rec.setMappingQuality(0);
                sw.addAlignment(rec);
                continue;
            }
            // contained int PCR fragment
            if (rec.getAlignmentStart() >= fragment.getStart() && rec.getAlignmentEnd() <= fragment.getEnd()) {
                sw.addAlignment(rec);
                continue;
            }
            final ReadClipper readClipper = new ReadClipper();
            if (samProgramRecord.isPresent()) {
                readClipper.setProgramGroup(samProgramRecord.get().getId());
            }
            rec = readClipper.clip(rec, fragment);
            sw.addAlignment(rec);
        }
        progress.finish();
        return 0;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(iter);
        CloserUtil.close(sw);
    }
}