Examples with CharSplitter com.github.lindenb.jvarkit.lang.CharSplitter used on opensource projects

Example 16 with CharSplitter

use of com.github.lindenb.jvarkit.lang.CharSplitter in project jvarkit by lindenb.

the class ContigNameConverter method fromPath.

public static ContigNameConverter fromPath(final Path mappingFile) {
    IOUtil.assertFileIsReadable(mappingFile);
    final MapBasedContigNameConverter mapper = new MapBasedContigNameConverter();
    mapper.name = mappingFile.getFileName().toString();
    BufferedReader in = null;
    try {
        final CharSplitter tab = CharSplitter.TAB;
        in = IOUtils.openPathForBufferedReading(mappingFile);
        String line;
        while ((line = in.readLine()) != null) {
            if (StringUtils.isBlank(line) || line.startsWith("#"))
                continue;
            final String[] tokens = tab.split(line);
            if (tokens.length != 2 || StringUtils.isBlank(tokens[0]) || StringUtils.isBlank(tokens[1])) {
                in.close();
                in = null;
                throw new IOException("Bad mapping line: \"" + line + "\" in " + mappingFile);
            }
            tokens[0] = tokens[0].trim();
            tokens[1] = tokens[1].trim();
            if (mapper.map.containsKey(tokens[0])) {
                in.close();
                throw new IOException("Mapping defined twice for: \"" + tokens[0] + "\"");
            }
            mapper.map.put(tokens[0], tokens[1]);
        }
        return mapper;
    } catch (final IOException err) {
        throw new RuntimeIOException(err);
    } finally {
        CloserUtil.close(in);
    }
}

Example 17 with CharSplitter

use of com.github.lindenb.jvarkit.lang.CharSplitter in project jvarkit by lindenb.

the class ConvertBamChromosomes method readMappingFile.

private Map<String, String> readMappingFile(final SAMSequenceDictionary dictIn, final SAMSequenceDictionary dictOut) throws IOException {
    final Map<String, String> mapper = new LinkedHashMap<>();
    BufferedReader in = null;
    final CharSplitter tab = CharSplitter.TAB;
    try {
        in = IOUtils.openPathForBufferedReading(this.mappingFile);
        String line;
        while ((line = in.readLine()) != null) {
            if (StringUtil.isBlank(line) || line.startsWith("#"))
                continue;
            final String[] tokens = tab.split(line);
            if (tokens.length != 2 || StringUtil.isBlank(tokens[0]) || StringUtil.isBlank(tokens[1])) {
                in.close();
                in = null;
                throw new IOException("Bad mapping line: \"" + line + "\"");
            }
            tokens[0] = tokens[0].trim();
            tokens[1] = tokens[1].trim();
            if (tokens[0].equals(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME) || tokens[1].equals(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME)) {
                in.close();
                throw new IOException("Bad name for: " + line);
            }
            if (dictIn.getSequence(tokens[0]) == null) {
                LOG.warn("Input dictionary doesn't contain " + tokens[0] + ", skipping");
                continue;
            }
            if (dictOut != null && dictOut.getSequence(tokens[1]) == null) {
                LOG.warn("Output dictionary doesn't contain " + tokens[1] + ", skipping");
                continue;
            }
            if (mapper.containsKey(tokens[0])) {
                in.close();
                throw new IOException("Mapping defined twice for src \"" + tokens[0] + "\"");
            }
            if (mapper.values().contains(tokens[1])) {
                throw new IOException("Mapping defined twice for dest \"" + tokens[1] + "\"");
            }
            mapper.put(tokens[0], tokens[1]);
        }
        return mapper;
    } finally {
        CloserUtil.close(in);
    }
}

Example 18 with CharSplitter

use of com.github.lindenb.jvarkit.lang.CharSplitter in project jvarkit by lindenb.

the class ConvertBamChromosomes method doWork.

@Override
public int doWork(final List<String> args) {
    final CharSplitter SEMICOLON_PAT = CharSplitter.SEMICOLON;
    final CharSplitter COMMA_PAT = CharSplitter.COMMA;
    if (this.dictSource == null && this.mappingFile == null) {
        LOG.error("dict source undefined and mapping file both undefined");
        return -1;
    }
    SamReader sr = null;
    SAMFileWriter sfw = null;
    try {
        final SamReaderFactory srf = super.createSamReaderFactory();
        if (this.faidx != null)
            srf.referenceSequence(this.faidx);
        final String input = oneFileOrNull(args);
        if (input == null) {
            sr = srf.open(SamInputResource.of(stdin()));
        } else {
            sr = srf.open(SamInputResource.of(input));
        }
        final SAMFileHeader inHeader = sr.getFileHeader();
        if (inHeader == null) {
            LOG.error("File header missing");
            return -1;
        }
        final SAMSequenceDictionary dictIn = SequenceDictionaryUtils.extractRequired(inHeader);
        if (dictIn.isEmpty()) {
            LOG.error("input Sequence dict is empty");
            return -1;
        }
        final SAMFileHeader outHeader = inHeader.clone();
        // create new sequence dict
        SAMSequenceDictionary dictOut = null;
        Map<String, String> contigMap = null;
        if (this.dictSource != null) {
            dictOut = SAMSequenceDictionaryExtractor.extractDictionary(this.dictSource);
        }
        if (this.mappingFile != null) {
            contigMap = this.readMappingFile(dictIn, dictOut);
        }
        if (dictOut == null && contigMap != null) {
            contigMap = this.readMappingFile(dictIn, dictOut);
            final List<SAMSequenceRecord> ssrs = new ArrayList<SAMSequenceRecord>(dictIn.size());
            for (final String ci : contigMap.keySet()) {
                final SAMSequenceRecord ssr1 = dictIn.getSequence(ci);
                if (ssr1 == null)
                    continue;
                final SAMSequenceRecord ssr2 = new SAMSequenceRecord(contigMap.get(ci), ssr1.getSequenceLength());
                for (final Map.Entry<String, String> atts : ssr1.getAttributes()) {
                    ssr2.setAttribute(atts.getKey(), atts.getValue());
                }
                ssrs.add(ssr2);
            }
            dictOut = new SAMSequenceDictionary(ssrs);
            this.mapper = ContigNameConverter.fromMap(contigMap);
        } else if (dictOut != null && contigMap == null) {
            this.mapper = ContigNameConverter.fromDictionaries(dictIn, dictOut);
        }
        if (this.mapper == null || dictOut == null) {
            LOG.error("Illegal state mapper==null or dict-out=null");
            return -1;
        }
        outHeader.setSequenceDictionary(dictOut);
        // check order of dictionaries, do we need to set the sort order ?
        int prev_out_index = -1;
        boolean output_is_sorted = true;
        for (int i = 0; i < dictIn.size(); i++) {
            final String si = dictIn.getSequence(i).getSequenceName();
            final String so = this.mapper.apply(si);
            if (so == null)
                continue;
            final int o_index = dictOut.getSequenceIndex(so);
            if (o_index < prev_out_index) {
                output_is_sorted = false;
                LOG.info("output will NOT be sorted");
                break;
            }
            prev_out_index = o_index;
        }
        if (!output_is_sorted) {
            outHeader.setSortOrder(SortOrder.unsorted);
        }
        sfw = this.writingBamArgs.openSamWriter(this.output, outHeader, true);
        long num_ignored = 0L;
        SAMRecordIterator iter = sr.iterator();
        while (iter.hasNext()) {
            final SAMRecord rec1 = iter.next();
            String newName1 = null;
            String newName2 = null;
            if (!SAMRecord.NO_ALIGNMENT_REFERENCE_NAME.equals(rec1.getReferenceName())) {
                newName1 = convert(rec1.getReferenceName(), dictOut);
            }
            if (rec1.getReadPairedFlag() && !SAMRecord.NO_ALIGNMENT_REFERENCE_NAME.equals(rec1.getMateReferenceName())) {
                newName2 = convert(rec1.getMateReferenceName(), dictOut);
            }
            rec1.setHeader(outHeader);
            if (!SAMRecord.NO_ALIGNMENT_REFERENCE_NAME.equals(rec1.getReferenceName())) {
                if (newName1 == null) {
                    ++num_ignored;
                    continue;
                } else {
                    rec1.setReferenceName(newName1);
                }
            }
            if (rec1.getReadPairedFlag() && !SAMRecord.NO_ALIGNMENT_REFERENCE_NAME.equals(rec1.getMateReferenceName())) {
                if (newName2 == null) {
                    ++num_ignored;
                    continue;
                }
                rec1.setMateReferenceName(newName2);
            }
            if (rec1.hasAttribute(SAMTag.SA.name())) {
                final Object sa = rec1.getStringAttribute(SAMTag.SA.name());
                if (sa != null && (sa instanceof String)) {
                    final String[] tokens = SEMICOLON_PAT.split(String.class.cast(sa));
                    final List<String> L = new ArrayList<>(tokens.length);
                    for (final String semiColonStr : tokens) {
                        final String[] commaStrs = COMMA_PAT.split(semiColonStr);
                        final String newctg = convert(commaStrs[0], dictOut);
                        if (newctg == null)
                            continue;
                        commaStrs[0] = newctg;
                        L.add(String.join(",", commaStrs));
                    }
                    if (L.isEmpty()) {
                        rec1.setAttribute(SAMTag.SA.name(), null);
                    } else {
                        rec1.setAttribute(SAMTag.SA.name(), String.join(";", L));
                    }
                }
            }
            sfw.addAlignment(rec1);
        }
        if (!this.unmappedChromosomes.isEmpty()) {
            LOG.warning("Unmapped chromosomes: " + unmappedChromosomes);
        }
        LOG.warning("num ignored read:" + num_ignored);
        return 0;
    } catch (final Throwable err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(sr);
        CloserUtil.close(sfw);
    }
}

Example 19 with CharSplitter

use of com.github.lindenb.jvarkit.lang.CharSplitter in project jvarkit by lindenb.

the class ConvertBedChromosomes method doWork.

@SuppressWarnings("resource")
protected int doWork(final BufferedReader in, PrintStream out) throws IOException {
    String line;
    final CharSplitter tab = CharSplitter.of(this.delimStr);
    final Pattern headerRegex = Pattern.compile(this.ignoreLinesPattern);
    while ((line = in.readLine()) != null) {
        final Matcher match = headerRegex.matcher(line);
        if (match.find() && match.start() == 0) {
            out.println(line);
            continue;
        }
        boolean ok = true;
        final String[] tokens = tab.split(line);
        for (final int chromColumn0 : this.chromColumns0) {
            if (chromColumn0 < 0 || chromColumn0 >= tokens.length) {
                ok = false;
                continue;
            }
            final String chrom = this.customMapping.apply(tokens[chromColumn0]);
            if (StringUtils.isBlank(chrom)) {
                if (this.unmappedChromosomes.add(tokens[chromColumn0])) {
                    LOG.warn("cannot convert " + tokens[chromColumn0]);
                }
                ok = false;
                continue;
            }
            tokens[chromColumn0] = chrom;
        }
        if (!ok) {
            switch(this.onNotFound) {
                case RAISE_EXCEPTION:
                    throw new IOException("Cannot convert chrom in : " + line);
                case SKIP:
                    continue;
                case RETURN_ORIGINAL:
                    break;
            }
        }
        out.println(String.join(String.valueOf(tab.getDelimiter()), tokens));
    }
    out.flush();
    return 0;
}

Example 20 with CharSplitter

use of com.github.lindenb.jvarkit.lang.CharSplitter in project jvarkit by lindenb.

the class BimToVcf method doWork.

@Override
public int doWork(final List<String> args) {
    VariantContextWriter w = null;
    BufferedReader r = null;
    ReferenceSequenceFile faidx = null;
    GenomicSequence genomic = null;
    long number_non_snvs = 0L;
    try {
        faidx = ReferenceSequenceFileFactory.getReferenceSequenceFile(this.faidx);
        final SAMSequenceDictionary dict = SequenceDictionaryUtils.extractRequired(faidx);
        this.writingVariants.dictionary(dict);
        r = super.openBufferedReader(oneFileOrNull(args));
        final Set<VCFHeaderLine> headerLines = new HashSet<>();
        final VCFInfoHeaderLine morgan = new VCFInfoHeaderLine("MORGAN", 1, VCFHeaderLineType.Float, "Centimorgan");
        final VCFInfoHeaderLine svtype = new VCFInfoHeaderLine("SVTYPE", 1, VCFHeaderLineType.String, "Variation type");
        VCFStandardHeaderLines.addStandardInfoLines(headerLines, false, "");
        // super.addMetaData(headerLines);
        headerLines.add(morgan);
        headerLines.add(svtype);
        final List<String> genotypeSampleNames = Collections.emptyList();
        final VCFHeader header = new VCFHeader(headerLines, genotypeSampleNames);
        header.setSequenceDictionary(dict);
        w = this.writingVariants.open(this.outputFile);
        w.writeHeader(header);
        final CharSplitter tab = CharSplitter.TAB;
        String line;
        final Predicate<String> iupacATGC = S -> AcidNucleics.isATGC(S);
        final List<String> convertCtg = Arrays.asList("23", "X", "23", "chrX", "24", "Y", "24", "chrY", "26", "MT", "26", "chrM");
        while ((line = r.readLine()) != null) {
            final String[] tokens = tab.split(line);
            if (tokens.length != 6) {
                throw new JvarkitException.TokenErrors(6, tokens);
            }
            Allele a1 = null;
            Allele a2 = null;
            Allele ref = null;
            final String contig = tokens[0];
            SAMSequenceRecord ssr = null;
            ssr = dict.getSequence(contig);
            for (int i = 0; ssr == null && i + 1 < convertCtg.size(); i += 2) {
                if (!convertCtg.get(i).equals(contig))
                    continue;
                ssr = dict.getSequence(convertCtg.get(i + 1));
            }
            if (ssr == null && contig.equals("25")) {
                LOG.warn("ignoring " + line);
                ++number_non_snvs;
                continue;
            }
            if (ssr == null) {
                throw new JvarkitException.ContigNotFoundInDictionary(contig, dict);
            }
            if (genomic == null || !ssr.getSequenceName().equals(genomic.getChrom())) {
                genomic = new GenomicSequence(faidx, ssr.getSequenceName());
            }
            int pos1 = Integer.parseInt(tokens[3]);
            if (tokens[4].equals("0"))
                tokens[4] = tokens[5];
            if (tokens[5].equals("0"))
                tokens[5] = tokens[4];
            final VariantContextBuilder vcb = new VariantContextBuilder();
            vcb.chr(ssr.getSequenceName());
            vcb.attribute(morgan.getID(), Float.parseFloat(tokens[2]));
            if (iupacATGC.test(tokens[4]) && iupacATGC.test(tokens[5])) {
                if (tokens[4].length() != 1 || tokens[5].length() != -1) {
                    LOG.warn("Skipping " + line + " because I only handle SNVs.");
                    number_non_snvs++;
                    continue;
                }
                final String refBase = String.valueOf(genomic.charAt(pos1 - 1));
                ref = Allele.create(refBase, true);
                a1 = refBase.equalsIgnoreCase(tokens[4]) ? ref : Allele.create(tokens[4], false);
                ;
                a2 = refBase.equalsIgnoreCase(tokens[5]) ? ref : Allele.create(tokens[5], false);
                final String type;
                if (a1.isReference() && a2.isReference()) {
                    type = "NOVARIATION";
                } else if (tokens[4].length() < tokens[5].length()) {
                    type = "INS";
                } else if (tokens[4].length() > tokens[5].length()) {
                    type = "DEL";
                } else {
                    type = "SNV";
                }
                vcb.attribute(svtype.getID(), type);
            } else if ((tokens[4].equals("-") && iupacATGC.test(tokens[5])) || (tokens[5].equals("-") && iupacATGC.test(tokens[4]))) {
                // shift left
                pos1--;
                String refBase = String.valueOf(genomic.charAt(pos1 - 1));
                a1 = Allele.create(refBase, false);
                ref = Allele.create(refBase + tokens[tokens[4].equals("-") ? 5 : 4], true);
                a2 = a1;
                vcb.attribute(svtype.getID(), "DEL");
            } else if (tokens[4].equals("-") && tokens[5].equals("-")) {
                // shift left
                pos1--;
                String refBase = String.valueOf(genomic.charAt(pos1 - 1));
                a1 = Allele.create(refBase, false);
                ref = Allele.create(refBase + genomic.charAt(pos1), true);
                a2 = a1;
                vcb.attribute(svtype.getID(), "DEL");
            } else {
                LOG.warn("Skipping " + line + ".");
                number_non_snvs++;
                continue;
            }
            final Set<Allele> alleles = new HashSet<>();
            alleles.add(ref);
            alleles.add(a1);
            alleles.add(a2);
            vcb.start(pos1);
            vcb.stop(pos1 + ref.length() - 1);
            if (!tokens[1].isEmpty())
                vcb.id(tokens[1]);
            vcb.alleles(alleles);
            w.add(vcb.make());
        }
        r.close();
        r = null;
        w.close();
        w = null;
        if (number_non_snvs > 0)
            LOG.warn("Number lines skipped:" + number_non_snvs);
        return 0;
    } catch (final Exception e) {
        LOG.error(e);
        return -1;
    } finally {
        CloserUtil.close(faidx);
        CloserUtil.close(w);
        CloserUtil.close(r);
    }
}