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

Example 26 with SAMFileWriter

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

the class BlastToSam method doWork.

@Override
public int doWork(List<String> args) {
    if (this.faidx == null || !this.faidx.exists() || !this.faidx.isFile()) {
        LOG.error("Option -R was not defined or dictionary missing");
        return -1;
    }
    final boolean interleaved_input = this.EXPECTED_SIZE > 0;
    final int maxRecordsInRam = 5000;
    SAMFileWriter sfw = null;
    XMLEventReader rx = null;
    final SAMFileWriterFactory sfwf = new SAMFileWriterFactory();
    sfwf.setCreateIndex(false);
    sfwf.setMaxRecordsInRam(maxRecordsInRam);
    sfwf.setCreateMd5File(false);
    sfwf.setUseAsyncIo(false);
    final SAMFileHeader header = new SAMFileHeader();
    try {
        LOG.info("opening " + faidx);
        this.dictionary = SAMSequenceDictionaryExtractor.extractDictionary(faidx);
        header.setSortOrder(SortOrder.unsorted);
        header.setSequenceDictionary(this.dictionary);
        final JAXBContext jc = JAXBContext.newInstance("gov.nih.nlm.ncbi.blast");
        this.unmarshaller = jc.createUnmarshaller();
        final XMLInputFactory xmlInputFactory = XMLInputFactory.newFactory();
        xmlInputFactory.setProperty(XMLInputFactory.IS_NAMESPACE_AWARE, Boolean.FALSE);
        xmlInputFactory.setProperty(XMLInputFactory.IS_COALESCING, Boolean.TRUE);
        xmlInputFactory.setProperty(XMLInputFactory.IS_REPLACING_ENTITY_REFERENCES, Boolean.TRUE);
        xmlInputFactory.setProperty(XMLInputFactory.IS_SUPPORTING_EXTERNAL_ENTITIES, Boolean.FALSE);
        xmlInputFactory.setXMLResolver(new XMLResolver() {

            @Override
            public Object resolveEntity(String arg0, String arg1, String arg2, String arg3) throws XMLStreamException {
                LOG.info("resolveEntity:" + arg0 + "/" + arg1 + "/" + arg2);
                return null;
            }
        });
        final String inputName = oneFileOrNull(args);
        if (inputName == null) {
            LOG.info("Reading from stdin");
            rx = xmlInputFactory.createXMLEventReader(stdin());
        } else if (args.size() == 1) {
            LOG.info("Reading from " + inputName);
            rx = xmlInputFactory.createXMLEventReader(IOUtils.openURIForBufferedReading(inputName));
        } else {
            LOG.error("Illegal number of args");
            return -1;
        }
        final SAMProgramRecord prg2 = header.createProgramRecord();
        fillHeader(rx, prg2);
        final SAMProgramRecord prg1 = header.createProgramRecord();
        prg1.setCommandLine(getProgramCommandLine());
        prg1.setProgramVersion(getVersion());
        prg1.setProgramName(getProgramName());
        prg1.setPreviousProgramGroupId(prg2.getId());
        final SAMReadGroupRecord rg1 = new SAMReadGroupRecord("g1");
        rg1.setLibrary("blast");
        rg1.setSample("blast");
        rg1.setDescription("blast");
        header.addReadGroup(rg1);
        sfw = this.writingBamArgs.openSAMFileWriter(outputFile, header, true);
        if (interleaved_input) {
            run_paired(sfw, rx, header);
        } else {
            run_single(sfw, rx, header);
        }
        return RETURN_OK;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(sfw);
        CloserUtil.close(rx);
    }
}

Example 27 with SAMFileWriter

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

the class BamStage method doMenuSaveAs.

@Override
protected void doMenuSaveAs() {
    final FileChooser fc = owner.newFileChooser();
    fc.getExtensionFilters().addAll(EXTENSION_FILTERS);
    final File saveAs = owner.updateLastDir(fc.showSaveDialog(this));
    if (saveAs == null)
        return;
    if (!saveAs.getName().endsWith(".bam")) {
        final Alert alert = new Alert(AlertType.ERROR, "Output should end with .bam", ButtonType.OK);
        alert.showAndWait();
        return;
    }
    Optional<BamJavascripFilter> bamjsfilter = Optional.empty();
    if (this.owner.javascriptCompiler.isPresent() && !this.javascriptArea.getText().trim().isEmpty()) {
        try {
            bamjsfilter = Optional.of(new BamJavascripFilter(this.getBamFile().getHeader(), Optional.of(this.owner.javascriptCompiler.get().compile(this.javascriptArea.getText()))));
        } catch (final Exception err) {
            JfxNgs.showExceptionDialog(this, err);
            bamjsfilter = Optional.empty();
            return;
        }
    }
    final Predicate<SAMRecord> flagfilter = makeFlagPredicate();
    final SAMFileWriterFactory swf = new SAMFileWriterFactory();
    swf.setCreateIndex(true);
    CloseableIterator<SAMRecord> iter = null;
    SAMFileWriter w = null;
    try {
        final SAMFileHeader h2 = this.getBamFile().getHeader().clone();
        h2.addComment("Generated with JfxNgs. javascript was: " + this.javascriptArea.getText().trim().replaceAll("[\n\t\r ]+", " "));
        w = swf.makeBAMWriter(h2, true, saveAs);
        iter = new LogCloseableIterator(this.getBamFile().iterator(), null);
        while (iter.hasNext()) {
            final SAMRecord rec = iter.next();
            if (!flagfilter.test(rec))
                continue;
            if (bamjsfilter.isPresent()) {
                if (bamjsfilter.get().eval(rec) == null)
                    continue;
            }
            w.addAlignment(rec);
        }
        w.close();
        w = null;
        iter.close();
        iter = null;
        final Alert alert = new Alert(AlertType.CONFIRMATION, "Done", ButtonType.OK);
        alert.showAndWait();
    } catch (Exception err) {
        JfxNgs.showExceptionDialog(this, err);
        return;
    } finally {
        CloserUtil.close(iter);
        CloserUtil.close(w);
    }
}

Example 28 with SAMFileWriter

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

the class GBrowserHtml method doWork.

@Override
public int doWork(List<String> args) {
    final int DEFAULT_EXTEND_INTERVAL = 0;
    SamReader samReader = null;
    ZipOutputStream zout = null;
    BufferedReader bufReader = null;
    PrintWriter paramsWriter = null;
    JsonWriter paramsJsonWriter = null;
    String line;
    IndexedFastaSequenceFile faidx = null;
    long snapshot_id = 0L;
    final String inputName = oneFileOrNull(args);
    try {
        final SamJsonWriterFactory samJsonWriterFactory = SamJsonWriterFactory.newInstance().printHeader(true).printAttributes(false).printMate(true).printReadQualities(false).closeStreamAtEnd(false);
        if (this.outputFile != null) {
            if (!this.outputFile.getName().endsWith(".zip")) {
                LOG.error("Output file should end with *.zip");
                return -1;
            }
        }
        bufReader = (inputName == null ? IOUtils.openStreamForBufferedReader(stdin()) : IOUtils.openURIForBufferedReading(inputName));
        final File tmpFile1 = File.createTempFile("gbrowse.", ".tmp");
        tmpFile1.deleteOnExit();
        final File tmpFile2 = File.createTempFile("gbrowse.", ".tmp");
        tmpFile2.deleteOnExit();
        paramsWriter = new PrintWriter(tmpFile2);
        paramsWriter.print("var config=");
        paramsWriter.flush();
        paramsJsonWriter = new JsonWriter(paramsWriter);
        paramsJsonWriter.beginArray();
        zout = new ZipOutputStream(super.openFileOrStdoutAsStream(this.outputFile));
        File bamFile = null;
        File faidxFile = null;
        String sampleName = null;
        int extend_interval = DEFAULT_EXTEND_INTERVAL;
        String title = null;
        Interval interval = null;
        while ((line = bufReader.readLine()) != null) {
            LOG.info(line);
            if (line.isEmpty() || line.startsWith("#"))
                continue;
            final int eq = line.indexOf("=");
            final String key = (eq == -1 ? "" : line.substring(0, eq).toLowerCase().trim());
            final String value = (eq == -1 ? "" : line.substring(eq + 1).trim());
            if (key.equals("bam")) {
                if (samReader != null)
                    samReader.close();
                samReader = null;
                bamFile = (value.isEmpty() ? null : new File(value));
            } else if (key.equals("sample")) {
                sampleName = (value.isEmpty() ? null : value);
            } else if (key.equals("title")) {
                title = (value.isEmpty() ? null : value);
            } else if (key.equals("ref") || key.equals("fasta")) {
                if (faidx != null)
                    faidx.close();
                faidx = null;
                faidxFile = (value.isEmpty() ? null : new File(value));
            } else if (key.equals("extend")) {
                extend_interval = (value.isEmpty() ? DEFAULT_EXTEND_INTERVAL : Integer.parseInt(value));
            } else if (key.equals("position") || key.equals("location") || key.equals("interval") || key.equals("goto")) {
                Pattern pat1 = Pattern.compile("([^\\:]+)\\:([\\d,]+)");
                Matcher matcher = pat1.matcher(value);
                if (matcher.matches()) {
                    String c = matcher.group(1);
                    int pos = Integer.parseInt(matcher.group(2).replaceAll("[,]", ""));
                    interval = new Interval(c, Math.max(1, pos - extend_interval), pos + extend_interval);
                    continue;
                }
                pat1 = Pattern.compile("([^\\:]+)\\:([\\d,]+)\\-([\\d,]+)");
                matcher = pat1.matcher(value);
                if (matcher.matches()) {
                    String c = matcher.group(1);
                    int B = Integer.parseInt(matcher.group(2).replaceAll("[,]", ""));
                    int E = Integer.parseInt(matcher.group(3).replaceAll("[,]", ""));
                    if (B > E) {
                        LOG.error("bad interval :" + line);
                        return -1;
                    }
                    interval = new Interval(c, Math.max(1, B - extend_interval), E + extend_interval);
                    continue;
                }
                pat1 = Pattern.compile("([^\\:]+)\\:([\\d,]+)\\+([\\d,]+)");
                matcher = pat1.matcher(value);
                if (matcher.matches()) {
                    String c = matcher.group(1);
                    int B = Integer.parseInt(matcher.group(2).replaceAll("[,]", ""));
                    int x = Integer.parseInt(matcher.group(3).replaceAll("[,]", ""));
                    interval = new Interval(c, Math.max(1, B - (x + extend_interval)), B + (x + extend_interval));
                    continue;
                }
                LOG.error("bad interval :" + line);
                return -1;
            } else if (line.toLowerCase().equals("snapshot")) {
                if (interval == null) {
                    LOG.error("No interval defined!");
                    continue;
                }
                if (bamFile == null) {
                    LOG.error("No BAM file defined!");
                    continue;
                }
                ++snapshot_id;
                LOG.info("open samFile " + bamFile);
                if (samReader == null) {
                    samReader = super.createSamReaderFactory().open(bamFile);
                }
                FileWriter jsonFileWriter = new FileWriter(tmpFile1);
                JsonWriter jsw = new JsonWriter(jsonFileWriter);
                jsw.beginObject();
                jsw.name("interval");
                jsw.beginObject();
                jsw.name("contig");
                jsw.value(interval.getContig());
                jsw.name("start");
                jsw.value(interval.getStart());
                jsw.name("end");
                jsw.value(interval.getEnd());
                jsw.endObject();
                if (faidxFile != null) {
                    if (faidx == null) {
                        faidx = new IndexedFastaSequenceFile(faidxFile);
                    }
                    ReferenceSequence dna = faidx.getSubsequenceAt(interval.getContig(), interval.getStart(), interval.getEnd());
                    jsw.name("reference");
                    jsw.value(dna.getBaseString());
                }
                jsw.name("sam");
                SAMFileWriter samFileWriter = samJsonWriterFactory.open(samReader.getFileHeader(), jsw);
                SAMRecordIterator samRecIter = samReader.queryOverlapping(interval.getContig(), interval.getStart(), interval.getEnd());
                while (samRecIter.hasNext()) {
                    final SAMRecord rec = samRecIter.next();
                    if (sampleName != null && !sampleName.isEmpty()) {
                        SAMReadGroupRecord srg = rec.getReadGroup();
                        if (srg == null)
                            continue;
                        if (!sampleName.equals(srg.getSample()))
                            continue;
                    }
                    if (rec.getReadUnmappedFlag())
                        continue;
                    samFileWriter.addAlignment(rec);
                }
                samRecIter.close();
                samFileWriter.close();
                jsw.endObject();
                jsw.flush();
                jsw.close();
                jsonFileWriter.close();
                ZipEntry entry = new ZipEntry(this.prefix + "_snapshot." + String.format("%05d", snapshot_id) + ".json");
                zout.putNextEntry(entry);
                IOUtils.copyTo(tmpFile1, zout);
                zout.closeEntry();
                tmpFile1.delete();
                paramsJsonWriter.beginObject();
                paramsJsonWriter.name("title");
                paramsJsonWriter.value(title == null ? interval.getContig() + ":" + interval.getStart() + "-" + interval.getEnd() + (sampleName == null ? "" : " " + sampleName) : title);
                paramsJsonWriter.name("interval");
                paramsJsonWriter.beginObject();
                paramsJsonWriter.name("contig");
                paramsJsonWriter.value(interval.getContig());
                paramsJsonWriter.name("start");
                paramsJsonWriter.value(interval.getStart());
                paramsJsonWriter.name("end");
                paramsJsonWriter.value(interval.getEnd());
                paramsJsonWriter.endObject();
                if (sampleName != null && !sampleName.isEmpty()) {
                    paramsJsonWriter.name("sample");
                    paramsJsonWriter.value(sampleName);
                }
                paramsJsonWriter.name("href");
                paramsJsonWriter.value("_snapshot." + String.format("%05d", snapshot_id) + ".json");
                paramsJsonWriter.endObject();
            } else if (line.toLowerCase().equals("exit") || line.toLowerCase().equals("quit")) {
                break;
            }
        }
        bufReader.close();
        bufReader = null;
        for (final String jssrc : new String[] { "gbrowse", "hershey", "samtools", "com.github.lindenb.jvarkit.tools.misc.GBrowserHtml" }) {
            InputStream is = this.getClass().getResourceAsStream("/META-INF/js/" + jssrc + ".js");
            if (is == null) {
                LOG.error("Cannot read resource /META-INF/js/" + jssrc + ".js");
                return -1;
            }
            ZipEntry entry = new ZipEntry(this.prefix + jssrc + ".js");
            entry.setComment("JAVASCRIPT SOURCE " + jssrc);
            zout.putNextEntry(entry);
            IOUtils.copyTo(is, zout);
            CloserUtil.close(is);
            zout.closeEntry();
        }
        // save params.js
        paramsJsonWriter.endArray();
        paramsJsonWriter.flush();
        paramsWriter.println(";");
        paramsWriter.flush();
        paramsJsonWriter.close();
        paramsWriter.close();
        zout.putNextEntry(new ZipEntry(this.prefix + "config.js"));
        IOUtils.copyTo(tmpFile2, zout);
        zout.closeEntry();
        tmpFile2.delete();
        // save index.html
        zout.putNextEntry(new ZipEntry(this.prefix + "index.html"));
        XMLOutputFactory xof = XMLOutputFactory.newFactory();
        XMLStreamWriter w = xof.createXMLStreamWriter(zout, "UTF-8");
        w.writeStartElement("html");
        w.writeStartElement("head");
        w.writeEmptyElement("meta");
        w.writeAttribute("http-equiv", "Content-Type");
        w.writeAttribute("content", "text/html; charset=utf-8");
        w.writeEmptyElement("meta");
        w.writeAttribute("http-equiv", "author");
        w.writeAttribute("content", "Pierre Lindenbaum Phd @yokofakun");
        w.writeStartElement("title");
        w.writeCharacters(getProgramName() + ":" + getVersion());
        // title
        w.writeEndElement();
        w.writeStartElement("style");
        w.writeAttribute("type", "text/css");
        w.writeCharacters("body	{ color:rgb(50,50,50); margin:20px; padding:20px; font: 12pt Arial, Helvetica, sans-serif; }\n");
        w.writeCharacters("label { text-align:right;	 }\n");
        w.writeCharacters("button	{ border: 1px solid; background-image:-moz-linear-gradient( top, gray, lightgray ); }\n");
        w.writeCharacters("canvas { image-rendering:auto;}\n");
        w.writeCharacters(".me 	{ padding-top:100px; font-size:80%; }\n");
        // style
        w.writeEndElement();
        for (final String src : new String[] { "samtools", "gbrowse", "hershey", "config", "com.github.lindenb.jvarkit.tools.misc.GBrowserHtml" }) {
            w.writeStartElement("script");
            w.writeAttribute("type", "text/javascript");
            w.writeAttribute("language", "text/javascript");
            w.writeAttribute("src", src + ".js");
            w.writeCharacters("");
            // script
            w.writeEndElement();
        }
        // head
        w.writeEndElement();
        w.writeStartElement("body");
        w.writeStartElement("div");
        w.writeStartElement("button");
        w.writeAttribute("onclick", "changemenu(-1)");
        w.writeCharacters("prev");
        // button
        w.writeEndElement();
        w.writeStartElement("select");
        w.writeAttribute("id", "menu");
        // menu
        w.writeEndElement();
        w.writeStartElement("button");
        w.writeAttribute("onclick", "changemenu(+1)");
        w.writeCharacters("next");
        // button
        w.writeEndElement();
        // div
        w.writeEndElement();
        w.writeStartElement("div");
        w.writeAttribute("id", "flags");
        // div
        w.writeEndElement();
        w.writeStartElement("div");
        w.writeAttribute("style", "text-align:center;");
        w.writeStartElement("div");
        w.writeAttribute("style", "font-size:200%;margin:10px;");
        w.writeAttribute("id", "browserTitle");
        // div
        w.writeEndElement();
        w.writeStartElement("div");
        w.writeEmptyElement("canvas");
        w.writeAttribute("id", "canvasdoc");
        w.writeAttribute("width", "100");
        w.writeAttribute("height", "100");
        // div
        w.writeEndElement();
        // div
        w.writeEndElement();
        w.writeEmptyElement("hr");
        w.writeStartElement("div");
        w.writeAttribute("class", "me");
        w.writeCharacters("Pierre Lindenbaum PhD. ");
        w.writeStartElement("a");
        w.writeAttribute("href", "https://github.com/lindenb/jvarkit");
        w.writeCharacters("https://github.com/lindenb/jvarkit");
        w.writeEndElement();
        w.writeCharacters(". Tested with Firefox 45.0");
        w.writeEndElement();
        // body
        w.writeEndElement();
        // html
        w.writeEndElement();
        w.flush();
        w.close();
        w = null;
        zout.closeEntry();
        zout.finish();
        zout.close();
        return RETURN_OK;
    } catch (Throwable err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(paramsJsonWriter);
        CloserUtil.close(paramsWriter);
        CloserUtil.close(zout);
        CloserUtil.close(bufReader);
        CloserUtil.close(samReader);
        CloserUtil.close(faidx);
    }
}

Example 29 with SAMFileWriter

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

the class BamClipToInsertion method doWork.

@Override
public int doWork(final List<String> args) {
    SAMRecordIterator iter = null;
    SamReader sfr = null;
    SAMFileWriter sfw = null;
    try {
        sfr = super.openSamReader(oneFileOrNull(args));
        final SAMFileHeader header1 = sfr.getFileHeader();
        if (header1 == null) {
            LOG.error("File header missing");
            return -1;
        }
        if (header1.getSortOrder() != SortOrder.coordinate) {
            LOG.error("Input is not sorted on coordinate.");
            return -1;
        }
        final SAMFileHeader header2 = header1.clone();
        header2.addComment(getProgramName() + ":" + getVersion() + ":" + getProgramCommandLine());
        header2.setSortOrder(SortOrder.unsorted);
        sfw = this.writingBamArgs.openSAMFileWriter(output, header2, true);
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header1);
        iter = sfr.iterator();
        String curContig = null;
        LinkedList<SamAndCigar> buffer = new LinkedList<>();
        for (; ; ) {
            SAMRecord rec = null;
            if (iter.hasNext()) {
                rec = progress.watch(iter.next());
                // ignore unmapped reads
                if (rec.getReadUnmappedFlag()) {
                    sfw.addAlignment(rec);
                    continue;
                }
            }
            if (rec == null || (curContig != null && !curContig.equals(rec.getReferenceName()))) {
                for (final SamAndCigar r : buffer) sfw.addAlignment(r.getSAMRecord());
                buffer.clear();
                // we're done
                if (rec == null)
                    break;
                curContig = rec.getReferenceName();
            }
            final SamAndCigar sac = new SamAndCigar(rec);
            if (!sac.containsIorS) {
                sfw.addAlignment(rec);
                continue;
            }
            buffer.add(sac);
            int i = 0;
            while (i < buffer.size()) {
                final SamAndCigar ri = buffer.get(i);
                if (ri.getSAMRecord().getUnclippedEnd() < rec.getUnclippedStart()) {
                    for (int j = 0; j < buffer.size(); ++j) {
                        if (i == j)
                            continue;
                        ri.merge(buffer.get(j));
                    }
                    sfw.addAlignment(ri.build());
                    buffer.remove(i);
                } else {
                    ++i;
                }
            }
        }
        progress.finish();
        LOG.info("done");
        return RETURN_OK;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(iter);
        CloserUtil.close(sfr);
        CloserUtil.close(sfw);
    }
}

Example 30 with SAMFileWriter

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

the class BamTile method doWork.

@Override
public int doWork(final List<String> args) {
    SAMRecordIterator iter = null;
    SamReader sfr = null;
    SAMFileWriter sfw = null;
    try {
        sfr = openSamReader(oneFileOrNull(args));
        final SAMFileHeader header1 = sfr.getFileHeader();
        if (header1 == null) {
            LOG.error("File header missing");
            return -1;
        }
        if (header1.getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
            LOG.error("File header not sorted on coordinate");
            return -1;
        }
        final SAMFileHeader header2 = header1.clone();
        header2.addComment("BamTile:" + getVersion() + ":" + getProgramCommandLine());
        sfw = this.writingBamArgs.openSAMFileWriter(this.outputFile, header2, true);
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header1);
        iter = sfr.iterator();
        final LinkedList<SAMRecord> buffer = new LinkedList<>();
        for (; ; ) {
            SAMRecord rec = null;
            if (iter.hasNext()) {
                rec = progress.watch(iter.next());
                if (rec.getReadUnmappedFlag())
                    continue;
                if (this.filterOut.filterOut(rec))
                    continue;
                if (!buffer.isEmpty()) {
                    final SAMRecord last = buffer.getLast();
                    if (this.no_overlap) {
                        if (last.getReferenceIndex() == rec.getReferenceIndex() && last.getEnd() >= rec.getStart()) {
                            continue;
                        }
                    } else {
                        if (last.getReferenceIndex() == rec.getReferenceIndex() && last.getAlignmentStart() <= rec.getAlignmentStart() && last.getAlignmentEnd() >= rec.getAlignmentEnd()) {
                            continue;
                        }
                    }
                }
            }
            if (rec == null || (!buffer.isEmpty() && buffer.getLast().getReferenceIndex() != rec.getReferenceIndex())) {
                while (!buffer.isEmpty()) {
                    sfw.addAlignment(buffer.removeFirst());
                }
                if (rec == null)
                    break;
            }
            buffer.add(rec);
            if (!this.no_overlap && buffer.size() > 2) {
                final int index = buffer.size();
                final SAMRecord prev = buffer.get(index - 3);
                final SAMRecord curr = buffer.get(index - 2);
                final SAMRecord next = buffer.get(index - 1);
                if (prev.getAlignmentEnd() >= next.getAlignmentStart() || curr.getAlignmentEnd() <= prev.getAlignmentEnd()) {
                    buffer.remove(index - 2);
                } else if (curr.getAlignmentStart() == prev.getAlignmentStart() && curr.getAlignmentEnd() > prev.getAlignmentEnd()) {
                    buffer.remove(index - 3);
                }
            }
            while (buffer.size() > 3) {
                sfw.addAlignment(buffer.removeFirst());
            }
        }
        progress.finish();
        sfw.close();
        sfw = null;
        iter.close();
        iter = null;
        sfr.close();
        sfr = null;
        LOG.info("done");
        return RETURN_OK;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(iter);
        CloserUtil.close(sfr);
        CloserUtil.close(sfw);
    }
}