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

Example 21 with SAMFileWriter

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

the class TestUtils method sortBamOnQueryName.

protected File sortBamOnQueryName(final Path bamFile, final Predicate<SAMRecord> pred) throws IOException {
    File sortedBam = this.createTmpFile(".bam");
    SamReader sr = SamReaderFactory.makeDefault().open(bamFile);
    SAMFileHeader outHeader = sr.getFileHeader().clone();
    outHeader.setSortOrder(SortOrder.queryname);
    SAMFileWriter w = new SAMFileWriterFactory().makeBAMWriter(outHeader, false, sortedBam);
    sr.iterator().stream().filter(R -> pred == null ? true : pred.test(R)).forEach(R -> w.addAlignment(R));
    w.close();
    sr.close();
    return sortedBam;
}

Example 22 with SAMFileWriter

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

the class TestUtils method addClippingToBam.

protected File addClippingToBam(final File bamFile) throws IOException {
    final String bases = "ATGC";
    File clippedBam = this.createTmpFile(".bam");
    SamReader sr = SamReaderFactory.makeDefault().open(bamFile);
    SAMFileHeader inHeader = sr.getFileHeader();
    boolean createIndex = sr.hasIndex() && inHeader.getSortOrder().equals(SortOrder.coordinate);
    if (createIndex) {
        this.deleteFilesAtExit.add(new File(bamFile.getParentFile(), IOUtil.basename(clippedBam) + BAMIndex.BAMIndexSuffix));
    }
    final SAMFileWriter w = new SAMFileWriterFactory().setCreateIndex(createIndex).makeBAMWriter(inHeader, true, clippedBam);
    sr.iterator().stream().map(R -> {
        if (R.getReadUnmappedFlag() || R.getCigar() == null)
            return R;
        if (R.getCigar().isClipped())
            return R;
        if (R.getBaseQualities().equals(SAMRecord.NULL_QUALS))
            return R;
        if (R.getBaseQualityString().equals(SAMRecord.NULL_QUALS_STRING))
            return R;
        for (int side = 0; side < 2; side++) {
            final String cigar;
            boolean hard = this.random.nextBoolean();
            final int clipLen = 1 + this.random.nextInt(100);
            final StringBuilder seq = new StringBuilder();
            final StringBuilder qual = new StringBuilder();
            if (hard) {
                cigar = String.valueOf(clipLen) + "H";
            } else {
                cigar = String.valueOf(clipLen) + "S";
                for (int x = 0; x < clipLen; ++x) {
                    seq.append(bases.charAt(this.random.nextInt(bases.length())));
                    qual.append("#");
                }
            }
            if (side == 0) {
                R.setReadString(seq.toString() + R.getReadString());
                R.setBaseQualityString(qual.toString() + R.getBaseQualityString());
                R.setCigarString(cigar + R.getCigarString());
            } else {
                R.setCigarString(R.getCigarString() + cigar);
                R.setReadString(R.getReadString() + seq.toString());
                R.setBaseQualityString(R.getBaseQualityString() + qual.toString());
            }
        }
        return R;
    }).forEach(R -> w.addAlignment(R));
    w.close();
    sr.close();
    assertIsValidBam(bamFile);
    return bamFile;
}

Example 23 with SAMFileWriter

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

the class Biostar90204 method doWork.

@Override
public int doWork(final List<String> args) {
    if (this.suffix_length < 0) {
        LOG.error("Bad value of suffix_length:" + this.suffix_length);
        return -1;
    }
    if (this.record_per_file < 1L) {
        LOG.error("Bad value of record_per_file:" + this.record_per_file);
        return -1;
    }
    SAMFileWriter sfw = null;
    SAMRecordIterator iter = null;
    SamReader samFileReader = null;
    PrintWriter manifest = new PrintWriter(new NullOuputStream());
    try {
        samFileReader = super.openSamReader(oneFileOrNull(args));
        final SAMFileHeader header = samFileReader.getFileHeader();
        int split_file_number = 0;
        long nReads = 0L;
        iter = samFileReader.iterator();
        if (this.manifestFile != null) {
            manifest.close();
            manifest = new PrintWriter(manifestFile);
        }
        while (iter.hasNext()) {
            final SAMRecord rec = iter.next();
            if (this.samRecordFilter.filterOut(rec))
                continue;
            ++nReads;
            if (sfw == null) {
                split_file_number++;
                final String pathname = (this.prefix.isEmpty() ? "" : this.prefix + ".") + String.format("%0" + suffix_length + "d", split_file_number) + ".bam";
                final File out = new File(pathname);
                manifest.write(pathname);
                manifest.write("\t" + (nReads) + "\t");
                final SAMFileHeader header2 = header.clone();
                header2.addComment("SPLIT:" + split_file_number);
                header2.addComment("SPLIT:Starting from Read" + nReads);
                sfw = this.writingBamArgs.openSAMFileWriter(out, header2, true);
            }
            sfw.addAlignment(rec);
            if (nReads % record_per_file == 0) {
                sfw.close();
                manifest.write((nReads) + "\n");
                sfw = null;
            }
        }
        if (sfw != null) {
            sfw.close();
            manifest.write((nReads) + "\n");
        }
        manifest.flush();
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(manifest);
        CloserUtil.close(sfw);
        CloserUtil.close(iter);
        CloserUtil.close(samFileReader);
    }
    return 0;
}

Example 24 with SAMFileWriter

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

the class Biostar76892 method doWork.

@Override
public int doWork(final List<String> args) {
    SamReader sfr = null;
    SAMFileWriter sfw = null;
    try {
        sfr = super.openSamReader(oneFileOrNull(args));
        sfw = writingBamArgs.openSAMFileWriter(this.outputFile, sfr.getFileHeader(), true);
        long nRecords = 0;
        final List<SAMRecord> buffer = new ArrayList<SAMRecord>();
        SAMRecordIterator iter = sfr.iterator();
        for (; ; ) {
            SAMRecord rec = null;
            // get next record
            if (iter.hasNext()) {
                rec = iter.next();
                ++nRecords;
                if (nRecords % 1000000 == 0)
                    LOG.info("records: " + nRecords);
                if (!rec.getReadPairedFlag() || rec.getReadUnmappedFlag() || rec.getMateUnmappedFlag() || rec.getProperPairFlag() || rec.getReferenceIndex() != rec.getMateReferenceIndex() || rec.getReadNegativeStrandFlag() == !rec.getMateNegativeStrandFlag()) {
                    if (!onlySaveFixed)
                        sfw.addAlignment(rec);
                    continue;
                }
            }
            if (rec != null) {
                int i = 0;
                // cleanup buffer
                int mate_index = -1;
                while (i < buffer.size()) {
                    SAMRecord prev = buffer.get(i);
                    if (prev.getReferenceIndex() != rec.getReferenceIndex() || prev.getAlignmentEnd() + distance < rec.getAlignmentStart()) {
                        if (!onlySaveFixed)
                            sfw.addAlignment(prev);
                        buffer.remove(i);
                    } else if (prev.getReadName().equals(rec.getReadName()) && ((prev.getFirstOfPairFlag() && rec.getSecondOfPairFlag()) || (rec.getFirstOfPairFlag() && prev.getSecondOfPairFlag()))) {
                        mate_index = i;
                        ++i;
                    } else {
                        ++i;
                    }
                }
                if (mate_index == -1) {
                    buffer.add(rec);
                } else {
                    final SAMRecord mate = buffer.get(mate_index);
                    buffer.remove(mate_index);
                    LOG.info("changing " + rec + " " + mate);
                    if (mate.getReadNegativeStrandFlag()) {
                        mate.setReadNegativeStrandFlag(false);
                        rec.setMateNegativeStrandFlag(mate.getReadNegativeStrandFlag());
                    } else {
                        rec.setReadNegativeStrandFlag(false);
                        mate.setMateNegativeStrandFlag(rec.getReadNegativeStrandFlag());
                    }
                    if (!mate.getReadFailsVendorQualityCheckFlag() && !rec.getReadFailsVendorQualityCheckFlag()) {
                        mate.setProperPairFlag(true);
                        rec.setProperPairFlag(true);
                    }
                    mate.setAttribute("rv", 1);
                    rec.setAttribute("rv", 1);
                    sfw.addAlignment(mate);
                    sfw.addAlignment(rec);
                }
            } else {
                for (final SAMRecord r : buffer) {
                    if (!onlySaveFixed)
                        sfw.addAlignment(r);
                }
                break;
            }
        }
        LOG.info("done");
        sfw.close();
        return RETURN_OK;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(sfw);
        CloserUtil.close(sfr);
    }
}

Example 25 with SAMFileWriter

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

the class Biostar78400 method doWork.

@Override
public int doWork(List<String> args) {
    if (this.XML == null) {
        LOG.error("XML file missing");
        return -1;
    }
    final Map<String, Map<Integer, String>> flowcell2lane2id = new HashMap<String, Map<Integer, String>>();
    SamReader sfr = null;
    SAMFileWriter sfw = null;
    try {
        final Pattern readNameSignature = Pattern.compile(this.readNameSignatureStr);
        final JAXBContext context = JAXBContext.newInstance(ReadGroup.class, ReadGroupList.class);
        final Unmarshaller unmarshaller = context.createUnmarshaller();
        final ReadGroupList rgl = unmarshaller.unmarshal(new StreamSource(XML), ReadGroupList.class).getValue();
        if (rgl.flowcells.isEmpty()) {
            LOG.error("empty XML " + XML);
            return -1;
        }
        sfr = openSamReader(oneFileOrNull(args));
        final SAMFileHeader header = sfr.getFileHeader().clone();
        header.addComment("Processed with " + getProgramName());
        final Set<String> seenids = new HashSet<String>();
        final List<SAMReadGroupRecord> samReadGroupRecords = new ArrayList<SAMReadGroupRecord>();
        for (final FlowCell fc : rgl.flowcells) {
            final Map<Integer, String> lane2id = new HashMap<Integer, String>();
            for (final Lane lane : fc.lanes) {
                for (final ReadGroup rg : lane.readGroups) {
                    if (seenids.contains(rg.id)) {
                        LOG.error("Group id " + rg.id + " defined twice");
                        return -1;
                    }
                    seenids.add(rg.id);
                    // create the read group we'll be using
                    final SAMReadGroupRecord rgrec = new SAMReadGroupRecord(rg.id);
                    rgrec.setLibrary(rg.library);
                    rgrec.setPlatform(rg.platform);
                    rgrec.setSample(rg.sample);
                    rgrec.setPlatformUnit(rg.platformunit);
                    if (rg.center != null)
                        rgrec.setSequencingCenter(rg.center);
                    if (rg.description != null)
                        rgrec.setDescription(rg.description);
                    lane2id.put(lane.id, rg.id);
                    samReadGroupRecords.add(rgrec);
                }
            }
            if (flowcell2lane2id.containsKey(fc.name)) {
                LOG.error("FlowCell id " + fc.name + " defined twice in XML");
                return -1;
            }
            flowcell2lane2id.put(fc.name, lane2id);
        }
        header.setReadGroups(samReadGroupRecords);
        sfw = this.writingBamArgs.openSAMFileWriter(this.outputFile, header, true);
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header);
        final SAMRecordIterator iter = sfr.iterator();
        while (iter.hasNext()) {
            final SAMRecord rec = progress.watch(iter.next());
            final Matcher matcher = readNameSignature.matcher(rec.getReadName());
            final String flowcellStr;
            final String laneStr;
            if (matcher.matches()) {
                flowcellStr = matcher.group(1);
                laneStr = matcher.group(2);
            } else {
                LOG.error("Read name " + rec.getReadName() + " doesn't match regular expression " + readNameSignature.pattern() + ". please check options");
                return -1;
            }
            String RGID = null;
            final Map<Integer, String> lane2id = flowcell2lane2id.get(flowcellStr);
            if (lane2id == null)
                throw new RuntimeException("Cannot get flowcell/readgroup for " + rec.getReadName());
            try {
                RGID = lane2id.get(Integer.parseInt(laneStr));
            } catch (final Exception e) {
                LOG.error("bad lane-Id in " + rec.getReadName());
                return -1;
            }
            if (RGID == null) {
                throw new RuntimeException("Cannot get RGID for " + rec.getReadName() + " flowcell:" + flowcellStr + " lane2id:" + laneStr + " dict:" + lane2id);
            }
            rec.setAttribute(SAMTag.RG.name(), RGID);
            sfw.addAlignment(rec);
        }
        progress.finish();
        iter.close();
        LOG.info("done");
        return RETURN_OK;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(sfw);
        CloserUtil.close(sfr);
    }
}