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

Example 31 with SAMFileWriterFactory

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

the class SoftClipsToSplitReads method doWork.

@Override
protected int doWork() {
    log.debug("Setting language-neutral locale");
    java.util.Locale.setDefault(Locale.ROOT);
    validateParameters();
    GenomicProcessingContext pc = new GenomicProcessingContext(getFileSystemContext(), REFERENCE_SEQUENCE, getReference());
    pc.setCommandLineProgram(this);
    pc.setFilterDuplicates(IGNORE_DUPLICATES);
    SplitReadRealigner realigner = new SplitReadRealigner(pc);
    realigner.setMinSoftClipLength(MIN_CLIP_LENGTH);
    realigner.setMinSoftClipQuality(MIN_CLIP_QUAL);
    realigner.setProcessSecondaryAlignments(PROCESS_SECONDARY_ALIGNMENTS);
    realigner.setWorkerThreads(WORKER_THREADS);
    try {
        SamReaderFactory readerFactory = SamReaderFactory.make();
        SAMFileWriterFactory writerFactory = new SAMFileWriterFactory();
        if (ALIGNER_STREAMING) {
            ExternalProcessStreamingAligner aligner = new ExternalProcessStreamingAligner(readerFactory, ALIGNER_COMMAND_LINE, REFERENCE_SEQUENCE, WORKER_THREADS);
            realigner.createSupplementaryAlignments(aligner, INPUT, OUTPUT);
        } else {
            ExternalProcessFastqAligner aligner = new ExternalProcessFastqAligner(readerFactory, writerFactory, ALIGNER_COMMAND_LINE);
            realigner.createSupplementaryAlignments(aligner, INPUT, OUTPUT);
        }
    } catch (IOException e) {
        log.error(e);
        return -1;
    }
    return 0;
}

Example 32 with SAMFileWriterFactory

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

the class SubsetToMissing method doWork.

@Override
protected int doWork() {
    long stop = Long.MAX_VALUE;
    if (STOP_AFTER != null && (long) STOP_AFTER > 0) {
        stop = STOP_AFTER;
    }
    log.debug("Setting language-neutral locale");
    java.util.Locale.setDefault(Locale.ROOT);
    if (TMP_DIR == null || TMP_DIR.size() == 0) {
        TMP_DIR = Lists.newArrayList(new File("."));
    }
    SamReaderFactory factory = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
    SamReader input = factory.open(INPUT);
    Iterator<SAMRecord> intputit = new AsyncBufferedIterator<SAMRecord>(input.iterator(), 2, 16384);
    SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(input.getFileHeader(), true, OUTPUT);
    LongSet hashtable;
    if (PREALLOCATE != null) {
        log.info("Preallocating hash table");
        hashtable = new LongOpenHashBigSet(PREALLOCATE);
    } else {
        hashtable = new LongOpenHashBigSet();
    }
    for (File file : LOOKUP) {
        log.info("Loading lookup hashes for " + file.getAbsolutePath());
        SamReader lookup = factory.open(file);
        AsyncBufferedIterator<SAMRecord> it = new AsyncBufferedIterator<SAMRecord>(lookup.iterator(), 2, 16384);
        File cache = new File(file.getAbsolutePath() + ".SubsetToMissing.cache");
        if (cache.exists()) {
            log.info("Loading lookup hashes from cache");
            long n = stop;
            DataInputStream dis = null;
            try {
                long loadCount = 0;
                dis = new DataInputStream(new BufferedInputStream(new FileInputStream(cache)));
                while (n-- > 0) {
                    hashtable.add(dis.readLong());
                    if (loadCount % 10000000 == 0) {
                        log.info(String.format("Loaded %d from cache", loadCount));
                    }
                }
            } catch (EOFException e) {
                try {
                    if (dis != null)
                        dis.close();
                } catch (IOException e1) {
                    log.error(e1);
                }
            } catch (IOException e) {
                log.error(e);
            }
        } else {
            long n = stop;
            ProgressLoggingSAMRecordIterator loggedit = new ProgressLoggingSAMRecordIterator(it, new ProgressLogger(log));
            try {
                DataOutputStream dos = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(cache)));
                while (loggedit.hasNext() && n-- > 0) {
                    long recordhash = hash(loggedit.next());
                    hashtable.add(recordhash);
                    dos.writeLong(recordhash);
                }
                dos.close();
            } catch (Exception e) {
                log.error(e, "Failed to load lookup. Running with partial results");
            }
            loggedit.close();
        }
        it.close();
    }
    long filtered = 0;
    log.info("Processing input");
    intputit = new ProgressLoggingSAMRecordIterator(intputit, new ProgressLogger(log));
    long n = stop;
    while (intputit.hasNext() && n-- > 0) {
        SAMRecord r = intputit.next();
        if (!hashtable.contains(hash(r))) {
            out.addAlignment(r);
        } else {
            filtered++;
            if (filtered % 1000000 == 0) {
                log.info(String.format("Filtered %d reads", filtered));
            }
        }
    }
    log.info("Closing output");
    out.close();
    return 0;
}

Example 33 with SAMFileWriterFactory

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

the class Biostar78400Test method test01.

@Test
public void test01() throws IOException {
    final String flowcell = "HS20001259127";
    final String lane = "1";
    final File in = createTmpFile(".bam");
    SAMFileHeader header = new SAMFileHeader();
    header.setSortOrder(SortOrder.unsorted);
    SAMFileWriter sfw = new SAMFileWriterFactory().makeBAMWriter(header, true, in);
    DefaultSAMRecordFactory recfactory = new DefaultSAMRecordFactory();
    SAMRecord rec = recfactory.createSAMRecord(header);
    rec.setReadName(flowcell + ":" + lane + ":1210:15640:52255");
    rec.setReadString("GAATTC");
    rec.setBaseQualityString("222222");
    SAMUtils.makeReadUnmapped(rec);
    sfw.addAlignment(rec);
    sfw.close();
    assertIsValidBam(in);
    final File xml = createTmpFile(".xml");
    PrintWriter pw = new PrintWriter(xml);
    pw.println("<?xml version=\"1.0\"?><read-groups>" + "<flowcell name=\"" + flowcell + "\"><lane index=\"" + lane + "\">" + "<group ID=\"X1\"><library>L1</library><platform>P1</platform>" + "<sample>S1</sample><platformunit>PU1</platformunit>" + "<center>C1</center><description>blabla</description></group>" + "</lane></flowcell><flowcell name=\"HS20001259128\">" + "<lane index=\"2\"><group ID=\"x2\"><library>L2</library>" + "<platform>P2</platform><sample>S2</sample><platformunit>PU1</platformunit>" + "<center>C1</center><description>blabla</description></group></lane>" + "</flowcell></read-groups>");
    pw.flush();
    pw.close();
    assertIsXml(xml);
    final File out = createTmpFile(".bam");
    Assert.assertEquals(new Biostar78400().instanceMain(newCmd().add("-o").add(out).add("-x").add(xml).add(in).make()), 0);
    SamReader r = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.LENIENT).open(out);
    Assert.assertTrue(r.getFileHeader() != null);
    Assert.assertTrue(r.getFileHeader().getReadGroups() != null);
    Assert.assertFalse(r.getFileHeader().getReadGroups().isEmpty());
    SAMRecordIterator iter = r.iterator();
    Assert.assertTrue(iter.hasNext());
    rec = iter.next();
    SAMReadGroupRecord rg = rec.getReadGroup();
    Assert.assertNotNull(rg);
    Assert.assertEquals(rg.getId(), "X1");
    Assert.assertEquals(rg.getSample(), "S1");
    Assert.assertFalse(iter.hasNext());
    iter.close();
    r.close();
}