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

Example 11 with SAMFileWriter

use of htsjdk.samtools.SAMFileWriter in project hmftools by hartwigmedical.

the class BamSlicerApplication method sliceFromURLs.

private static void sliceFromURLs(@NotNull final URL indexUrl, @NotNull final URL bamUrl, @NotNull final CommandLine cmd) throws IOException {
    final File indexFile = downloadIndex(indexUrl);
    indexFile.deleteOnExit();
    final SamReader reader = SamReaderFactory.makeDefault().open(SamInputResource.of(bamUrl).index(indexFile));
    final SAMFileWriter writer = new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(reader.getFileHeader(), true, new File(cmd.getOptionValue(OUTPUT)));
    final BAMIndex bamIndex = new DiskBasedBAMFileIndex(indexFile, reader.getFileHeader().getSequenceDictionary(), false);
    final Optional<Pair<QueryInterval[], BAMFileSpan>> queryIntervalsAndSpan = queryIntervalsAndSpan(reader, bamIndex, cmd);
    final Optional<Chunk> unmappedChunk = getUnmappedChunk(bamIndex, HttpUtils.getHeaderField(bamUrl, "Content-Length"), cmd);
    final List<Chunk> sliceChunks = sliceChunks(queryIntervalsAndSpan, unmappedChunk);
    final SamReader cachingReader = createCachingReader(indexFile, bamUrl, cmd, sliceChunks);
    queryIntervalsAndSpan.ifPresent(pair -> {
        LOGGER.info("Slicing bam on bed regions...");
        final CloseableIterator<SAMRecord> bedIterator = getIterator(cachingReader, pair.getKey(), pair.getValue().toCoordinateArray());
        writeToSlice(writer, bedIterator);
        LOGGER.info("Done writing bed slices.");
    });
    unmappedChunk.ifPresent(chunk -> {
        LOGGER.info("Slicing unmapped reads...");
        final CloseableIterator<SAMRecord> unmappedIterator = cachingReader.queryUnmapped();
        writeToSlice(writer, unmappedIterator);
        LOGGER.info("Done writing unmapped reads.");
    });
    reader.close();
    writer.close();
    cachingReader.close();
}

Example 12 with SAMFileWriter

use of htsjdk.samtools.SAMFileWriter in project polyGembler by c-zhou.

the class SamFileExtract method run.

@Override
public void run() {
    // TODO Auto-generated method stub
    final SamReaderFactory factory = SamReaderFactory.makeDefault().enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS, SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS).validationStringency(ValidationStringency.SILENT);
    final SamReader inputSam = factory.open(new File(bam_in));
    final SAMFileHeader header = inputSam.getFileHeader();
    final SAMSequenceDictionary seqdic = header.getSequenceDictionary();
    final SAMFileHeader header_out = new SAMFileHeader();
    final SAMSequenceDictionary seqdic_out = new SAMSequenceDictionary();
    SAMRecordIterator iter = inputSam.iterator();
    File bed_file = new File(bed_in);
    final Set<String> extract = new HashSet<String>();
    try (BufferedReader br = new BufferedReader(new FileReader(bed_file))) {
        String line;
        while ((line = br.readLine()) != null) extract.add(line.split("\\s+")[0]);
    } catch (IOException e) {
        e.printStackTrace();
        System.exit(1);
    }
    header_out.setAttribute("VN", header.getAttribute("VN"));
    header_out.setAttribute("SO", header.getAttribute("SO"));
    List<SAMSequenceRecord> seqs = seqdic.getSequences();
    for (SAMSequenceRecord seq : seqs) if (extract.contains(seq.getSequenceName()))
        seqdic_out.addSequence(seq);
    header_out.setSequenceDictionary(seqdic_out);
    for (SAMReadGroupRecord rg : header.getReadGroups()) header_out.addReadGroup(rg);
    for (SAMProgramRecord pg : header.getProgramRecords()) header_out.addProgramRecord(pg);
    final SAMFileWriter outputSam = new SAMFileWriterFactory().makeSAMOrBAMWriter(header_out, true, new File(bam_out));
    while (iter.hasNext()) {
        SAMRecord rec = iter.next();
        if (extract.contains(rec.getReferenceName()))
            outputSam.addAlignment(rec);
    }
    iter.close();
    try {
        inputSam.close();
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    outputSam.close();
    System.err.println(bam_in + " return true");
}

Example 13 with SAMFileWriter

use of htsjdk.samtools.SAMFileWriter in project polyGembler by c-zhou.

the class SamFileFilter method run.

@Override
public void run() {
    // TODO Auto-generated method stub
    File folder = new File(input_dir);
    File[] listOfFiles = folder.listFiles(new FilenameFilter() {

        @Override
        public boolean accept(File dir, String name) {
            return name.endsWith(".bam");
        }
    });
    int bam_n = listOfFiles.length;
    this.initial_thread_pool();
    for (int i = 0; i < bam_n; i++) {
        executor.submit(new Runnable() {

            private String bam_file;

            @Override
            public void run() {
                // TODO Auto-generated method stub
                try {
                    final SamReaderFactory factory = SamReaderFactory.makeDefault().enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS, SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS).validationStringency(ValidationStringency.SILENT);
                    final SamReader inputSam = factory.open(new File(input_dir + "/" + bam_file));
                    final SAMFileWriter outputSam = new SAMFileWriterFactory().makeSAMOrBAMWriter(inputSam.getFileHeader(), true, new File(output_dir + "/" + bam_file));
                    final BufferedReader filter_br = Utils.getBufferedReader(filter_file);
                    SAMRecordIterator iter = inputSam.iterator();
                    String line = filter_br.readLine();
                    if (line == null) {
                        filter_br.close();
                        iter.close();
                        inputSam.close();
                        outputSam.close();
                        return;
                    }
                    String[] s = line.split("\\s+");
                    String chr = s[0];
                    long end_pos = Long.parseLong(s[1]);
                    SAMRecord samr;
                    while (iter.hasNext()) {
                        samr = iter.next();
                        if (samr.getReferenceName().equals(chr) && samr.getAlignmentEnd() < end_pos) {
                            outputSam.addAlignment(samr);
                            continue;
                        }
                        if (!samr.getReferenceName().equals(chr) || samr.getAlignmentStart() > end_pos) {
                            line = null;
                            while ((line = filter_br.readLine()) != null && end_pos < samr.getAlignmentStart()) {
                                s = line.split("\\s");
                                chr = s[0];
                                end_pos = Long.parseLong(s[1]);
                            }
                            if (line != null) {
                                if (samr.getReferenceName().equals(chr) && samr.getAlignmentEnd() < end_pos)
                                    outputSam.addAlignment(samr);
                            } else {
                                outputSam.addAlignment(samr);
                                while (iter.hasNext()) outputSam.addAlignment(iter.next());
                                break;
                            }
                        }
                    }
                    filter_br.close();
                    iter.close();
                    inputSam.close();
                    outputSam.close();
                } catch (Exception e) {
                    Thread t = Thread.currentThread();
                    t.getUncaughtExceptionHandler().uncaughtException(t, e);
                    e.printStackTrace();
                    executor.shutdown();
                    System.exit(1);
                }
            }

            public Runnable init(String bam_file) {
                // TODO Auto-generated method stub
                this.bam_file = bam_file;
                return this;
            }
        }.init(listOfFiles[i].getName()));
        throw new RuntimeException("incorrect tools!!!!");
    }
    this.waitFor();
}

Example 14 with SAMFileWriter

use of htsjdk.samtools.SAMFileWriter in project ASCIIGenome by dariober.

the class Utils method sortAndIndexSamOrBam.

/**
 * Sort and index input sam or bam.
 * @throws IOException
 */
public static void sortAndIndexSamOrBam(String inSamOrBam, String sortedBam, boolean deleteOnExit) throws IOException {
    /*  ------------------------------------------------------ */
    /* This chunk prepares SamReader from local bam or URL bam */
    UrlValidator urlValidator = new UrlValidator();
    SamReaderFactory srf = SamReaderFactory.make();
    srf.validationStringency(ValidationStringency.SILENT);
    SamReader samReader;
    if (urlValidator.isValid(inSamOrBam)) {
        samReader = SamReaderFactory.makeDefault().open(SamInputResource.of(new URL(inSamOrBam)));
    } else {
        samReader = srf.open(new File(inSamOrBam));
    }
    /*  ------------------------------------------------------ */
    samReader.getFileHeader().setSortOrder(SortOrder.coordinate);
    File out = new File(sortedBam);
    if (deleteOnExit) {
        out.deleteOnExit();
        File idx = new File(out.getAbsolutePath().replaceAll("\\.bam$", "") + ".bai");
        idx.deleteOnExit();
    }
    SAMFileWriter outputSam = new SAMFileWriterFactory().setCreateIndex(true).makeSAMOrBAMWriter(samReader.getFileHeader(), false, out);
    for (final SAMRecord samRecord : samReader) {
        outputSam.addAlignment(samRecord);
    }
    samReader.close();
    outputSam.close();
}

Example 15 with SAMFileWriter

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

the class StubFastqAligner method align.

@Override
public void align(File fastq, File output, File reference, int threads) throws IOException {
    SAMFileHeader header = context.getBasicSamHeader();
    try (FastqReader reader = new FastqReader(fastq)) {
        try (SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, true, output)) {
            for (FastqRecord fqr : reader) {
                SAMRecord source = nameLookup.get(fqr.getReadName());
                SAMRecord r = new SAMRecord(header);
                r.setReadName(fqr.getReadName());
                r.setReadBases(fqr.getReadString().getBytes());
                r.setBaseQualities(SAMUtils.fastqToPhred(fqr.getBaseQualityString()));
                if (source == null) {
                    r.setReadUnmappedFlag(true);
                } else {
                    ChimericAlignment aln = map.get(fqr.getReadName());
                    r.setReferenceName(aln.rname);
                    r.setAlignmentStart(aln.pos);
                    r.setCigar(aln.cigar);
                    r.setMappingQuality(aln.mapq);
                    r.setAttribute("NM", aln.nm);
                    if (aln.isNegativeStrand) {
                        SequenceUtil.reverseComplement(r.getReadBases());
                        ArrayUtils.reverse(r.getBaseQualities());
                    }
                }
                writer.addAlignment(r);
            }
        }
    }
}