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

Example 26 with SAMFileWriterFactory

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

the class TenXMoleculeStats method runBCSortedStats.

public void runBCSortedStats() {
    // TODO Auto-generated method stub
    final SamReader inputSam = factory.open(new File(this.in_bam));
    final SAMSequenceDictionary seqDic = inputSam.getFileHeader().getSequenceDictionary();
    mappedReadsOnChromosome = new long[seqDic.size()];
    /**
     *		try {
     *			oos = Utils.getGZIPBufferedWriter(out_stats);
     *		} catch (IOException e1) {
     *			// TODO Auto-generated catch block
     *			e1.printStackTrace();
     *		}
     */
    oos = Utils.getBufferedWriter(out_stats + ".txt");
    oob = new SAMFileWriterFactory().makeSAMOrBAMWriter(inputSam.getFileHeader(), true, new File(out_stats + ".bam"));
    SAMRecordIterator iter = inputSam.iterator();
    SAMRecord record = iter.next();
    String bc_str;
    this.initial_thread_pool();
    while (record != null) {
        // if(mappedReads%1000000==0) myLogger.info(mappedReads+" mapped records processed.");
        List<SAMRecord> bc_records = new ArrayList<SAMRecord>();
        bc_str = record.getStringAttribute("BX");
        this.processRecord(bc_records, record);
        while (bc_str == null) {
            record = iter.hasNext() ? iter.next() : null;
            if (record == null)
                break;
            this.processRecord(bc_records, record);
            bc_str = record.getStringAttribute("BX");
        }
        if (bc_str == null)
            continue;
        while (true) {
            record = iter.hasNext() ? iter.next() : null;
            if (record == null)
                break;
            if (bc_str.equals(record.getStringAttribute("BX"))) {
                this.processRecord(bc_records, record);
            } else
                break;
        }
        if (bc_records.isEmpty())
            continue;
        readsOnBarcode.put(bc_records.get(0).getStringAttribute("BX"), bc_records.size());
        executor.submit(new MoleculeConstructor(bc_records));
    }
    try {
        iter.close();
        inputSam.close();
        this.waitFor();
        oos.close();
        oob.close();
        BufferedWriter bw_summary = Utils.getBufferedWriter(this.out_stats + ".summary");
        bw_summary.write("##Reads     mapped: " + mappedReads + "\n");
        bw_summary.write("##Reads   unmapped: " + unmappedReads + "\n");
        bw_summary.write("##Reads duplicated: " + duplicatedReads + "\n");
        bw_summary.write("##Reads  bad pairs: " + badpaired + "\n");
        bw_summary.write("##Reads by pseudo-chromosomes:\n");
        for (int i = 0; i < mappedReadsOnChromosome.length; i++) {
            bw_summary.write(" #" + seqDic.getSequence(i).getSequenceName() + " " + mappedReadsOnChromosome[i] + "\n");
        }
        bw_summary.write("##Reads by barcodes:\n");
        for (Map.Entry<String, Integer> entry : readsOnBarcode.entrySet()) {
            bw_summary.write(" #" + entry.getKey() + " " + entry.getValue() + "\n");
        }
        bw_summary.close();
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    myLogger.info("Completed. " + counter + " bam records processed.");
}

Example 27 with SAMFileWriterFactory

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

the class TenXSamtools method runSort.

private void runSort() {
    // 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(this.bam_in));
    final SAMFileHeader sort_header = inputSam.getFileHeader();
    switch(this.sort_order) {
        case coordinate:
            sort_header.setSortOrder(SortOrder.coordinate);
            break;
        case queryname:
            sort_header.setSortOrder(SortOrder.queryname);
            break;
        case barcode:
            sort_header.setSortOrder(SortOrder.unknown);
            break;
    }
    SAMRecordIterator iter = inputSam.iterator();
    long record_inCount = 0;
    SAMRecord[] buff = new SAMRecord[this.batch_size];
    int k = 0;
    SAMRecord temp = iter.hasNext() ? iter.next() : null;
    this.initial_thread_pool();
    while (temp != null) {
        buff[k++] = temp;
        record_inCount++;
        temp = iter.hasNext() ? iter.next() : null;
        if (k == this.batch_size || temp == null) {
            executor.submit(new Runnable() {

                private SAMRecord[] records;

                @Override
                public void run() {
                    // TODO Auto-generated method stub
                    try {
                        Arrays.sort(records, comprator);
                        final SAMFileWriter outputSam;
                        synchronized (lock) {
                            outputSam = new SAMFileWriterFactory().makeSAMOrBAMWriter(sort_header, true, new File(bam_out + String.format("%08d", batch++)));
                        }
                        int count = 0;
                        for (SAMRecord record : records) {
                            if (record != null) {
                                count++;
                                outputSam.addAlignment(record);
                            }
                        }
                        outputSam.close();
                        synchronized (lock) {
                            record_count += count;
                        }
                        myLogger.info("[" + Thread.currentThread().getName() + "] " + record_count + " records processed.");
                    } catch (Exception e) {
                        Thread t = Thread.currentThread();
                        t.getUncaughtExceptionHandler().uncaughtException(t, e);
                        e.printStackTrace();
                        executor.shutdown();
                        System.exit(1);
                    }
                }

                public Runnable init(SAMRecord[] buff) {
                    // TODO Auto-generated method stub
                    this.records = buff;
                    return (this);
                }
            }.init(buff));
            k = 0;
            buff = new SAMRecord[this.batch_size];
        }
    }
    iter.close();
    try {
        inputSam.close();
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    myLogger.info(record_inCount + " records read from " + this.bam_in);
    this.waitFor();
    // merge all batches
    myLogger.info("Merge " + batch + " files.");
    final SAMFileWriter outputSam = new SAMFileWriterFactory().makeSAMOrBAMWriter(sort_header, true, new File(this.bam_out));
    final SamReader[] batchSam = new SamReader[batch];
    final SAMRecordIterator[] iterSam = new SAMRecordIterator[batch];
    final boolean[] reachFileEnd = new boolean[batch];
    final TreeMap<SAMRecord, Integer> treeMap = new TreeMap<SAMRecord, Integer>(this.comprator);
    for (int i = 0; i != batch; i++) {
        batchSam[i] = factory.open(new File(this.bam_out + String.format("%08d", i)));
        iterSam[i] = batchSam[i].iterator();
        if (iterSam[i].hasNext())
            treeMap.put(iterSam[i].next(), i);
        reachFileEnd[i] = !iterSam[i].hasNext();
    }
    Entry<SAMRecord, Integer> firstEntry;
    int bch, nReachFileEnd = 0;
    for (boolean b : reachFileEnd) if (b)
        nReachFileEnd++;
    long record_outCount = 0;
    while (!treeMap.isEmpty()) {
        firstEntry = treeMap.pollFirstEntry();
        outputSam.addAlignment(firstEntry.getKey());
        record_outCount++;
        bch = firstEntry.getValue();
        if (!reachFileEnd[bch]) {
            treeMap.put(iterSam[bch].next(), bch);
            if (!iterSam[bch].hasNext()) {
                reachFileEnd[bch] = true;
                nReachFileEnd++;
            }
        }
        if (treeMap.isEmpty() && nReachFileEnd != batch) {
            for (int i = 0; i != batch; i++) {
                if (!reachFileEnd[i]) {
                    treeMap.put(iterSam[i].next(), i);
                    if (!iterSam[i].hasNext()) {
                        reachFileEnd[i] = true;
                        nReachFileEnd++;
                    }
                }
            }
        }
    }
    try {
        outputSam.close();
        for (int i = 0; i != batch; i++) {
            iterSam[i].close();
            batchSam[i].close();
            new File(this.bam_out + String.format("%08d", i)).delete();
        }
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    myLogger.info(record_outCount + " records written to " + this.bam_out);
}

Example 28 with SAMFileWriterFactory

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

the class IntermediateFilesTest method createBAM.

public void createBAM(File file, SAMFileHeader header, SAMRecord... data) {
    SAMFileWriter writer = new SAMFileWriterFactory().setCreateIndex(true).makeSAMOrBAMWriter(header, true, file);
    if (header.getSortOrder() == SortOrder.coordinate) {
        SortingCollection<SAMRecord> presort = SortingCollection.newInstance(SAMRecord.class, new BAMRecordCodec(header), new SAMRecordCoordinateComparator(), 100000000, testFolder.getRoot());
        for (SAMRecord r : data) {
            presort.add(r);
        }
        presort.doneAdding();
        for (SAMRecord r : presort) {
            writer.addAlignment(r);
        }
    } else {
        for (SAMRecord r : data) {
            writer.addAlignment(r);
        }
    }
    writer.close();
}

Example 29 with SAMFileWriterFactory

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

the class VcfBreakendToReadPair method writeVisualisationBam.

public void writeVisualisationBam(GenomicProcessingContext pc, File vcf, File bam, File bamFiltered) throws IOException {
    File working = FileSystemContext.getWorkingFileFor(bam);
    File workingFiltered = FileSystemContext.getWorkingFileFor(bamFiltered);
    VCFFileReader vcfReader = new VCFFileReader(vcf, false);
    CloseableIterator<VariantContext> it = vcfReader.iterator();
    SAMFileWriter writer = null;
    SAMFileWriter writerFiltered = null;
    try {
        SAMFileWriterFactory factory = pc.getSamFileWriterFactory(true);
        SAMFileHeader header = pc.getBasicSamHeader();
        writer = factory.makeSAMOrBAMWriter(header, false, working);
        writerFiltered = factory.makeSAMOrBAMWriter(header, false, workingFiltered);
        while (it.hasNext()) {
            IdsvVariantContext variant = IdsvVariantContext.create(pc, null, it.next());
            if (variant instanceof VariantContextDirectedBreakpoint) {
                VariantContextDirectedBreakpoint bp = (VariantContextDirectedBreakpoint) variant;
                if (bp.isFiltered()) {
                    writerFiltered.addAlignment(bp.asSamRecord(header));
                } else {
                    writer.addAlignment(bp.asSamRecord(header));
                }
            }
        }
        writer.close();
        writerFiltered.close();
        // Correct mate pairing since asSAMRecord() does not factor in mate anchor cigar
        new FixMate().fix(working, bam);
        new FixMate().fix(workingFiltered, bamFiltered);
    } finally {
        CloserUtil.close(writer);
        CloserUtil.close(writerFiltered);
        CloserUtil.close(it);
        CloserUtil.close(vcfReader);
        FileHelper.delete(working, true);
        FileHelper.delete(workingFiltered, true);
    }
}

Example 30 with SAMFileWriterFactory

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

the class MultipleSamFileCommandLineProgram method ensureSequenceDictionary.

public static void ensureSequenceDictionary(File fa) throws IOException {
    File output = new File(fa.getAbsolutePath() + ".dict");
    try (ReferenceSequenceFile reference = ReferenceSequenceFileFactory.getReferenceSequenceFile(fa)) {
        SAMSequenceDictionary dictionary = reference.getSequenceDictionary();
        if (dictionary == null) {
            log.info("Attempting to generate missing sequence dictionary for ", fa);
            try {
                final SAMSequenceDictionary sequences = new CreateSequenceDictionary().makeSequenceDictionary(fa);
                final SAMFileHeader samHeader = new SAMFileHeader();
                samHeader.setSequenceDictionary(sequences);
                try (SAMFileWriter samWriter = new SAMFileWriterFactory().makeSAMWriter(samHeader, false, output)) {
                }
            } catch (Exception e) {
                log.error("Missing sequence dictionary for ", fa, " and creation of sequencing dictionary failed.", "Please run the Picard tools CreateSequenceDictionary utility to create", output);
                throw e;
            }
            log.info("Created sequence dictionary ", output);
        } else {
            log.debug("Found sequence dictionary for ", fa);
        }
    }
}