Exemple #1
0
  /**
   * checks if the read has a platform tag in the readgroup equal to 'name'. Assumes that 'name' is
   * upper-cased.
   *
   * @param read the read to test
   * @param name the upper-cased platform name to test
   * @return whether or not name == PL tag in the read group of read
   */
  public static boolean isPlatformRead(SAMRecord read, String name) {

    SAMReadGroupRecord readGroup = read.getReadGroup();
    if (readGroup != null) {
      Object readPlatformAttr = readGroup.getAttribute("PL");
      if (readPlatformAttr != null) return readPlatformAttr.toString().toUpperCase().contains(name);
    }
    return false;
  }
  protected int doWork() {
    IoUtil.assertFileIsReadable(INPUT);
    IoUtil.assertFileIsWritable(OUTPUT);

    final SAMFileReader in = new SAMFileReader(INPUT);

    // create the read group we'll be using
    final SAMReadGroupRecord rg = new SAMReadGroupRecord(RGID);
    rg.setLibrary(RGLB);
    rg.setPlatform(RGPL);
    rg.setSample(RGSM);
    rg.setPlatformUnit(RGPU);
    if (RGCN != null) rg.setSequencingCenter(RGCN);
    if (RGDS != null) rg.setDescription(RGDS);
    if (RGDT != null) rg.setRunDate(RGDT);

    log.info(
        String.format(
            "Created read group ID=%s PL=%s LB=%s SM=%s%n",
            rg.getId(), rg.getPlatform(), rg.getLibrary(), rg.getSample()));

    // create the new header and output file
    final SAMFileHeader inHeader = in.getFileHeader();
    final SAMFileHeader outHeader = inHeader.clone();
    outHeader.setReadGroups(Arrays.asList(rg));
    if (SORT_ORDER != null) outHeader.setSortOrder(SORT_ORDER);

    final SAMFileWriter outWriter =
        new SAMFileWriterFactory()
            .makeSAMOrBAMWriter(
                outHeader, outHeader.getSortOrder() == inHeader.getSortOrder(), OUTPUT);

    final ProgressLogger progress = new ProgressLogger(log);
    for (final SAMRecord read : in) {
      read.setAttribute(SAMTag.RG.name(), RGID);
      outWriter.addAlignment(read);
      progress.record(read);
    }

    // cleanup
    in.close();
    outWriter.close();
    return 0;
  }
Exemple #3
0
 /**
  * Returns the sample name associated with the provided read's read group.
  *
  * @param read read whose sample name to retrieve
  * @param header SAM header containing read groups
  * @return the sample name for the provided read's read group as a String, or null if the read has
  *     no read group.
  */
 public static String getSampleName(final GATKRead read, final SAMFileHeader header) {
   final SAMReadGroupRecord readGroup = getSAMReadGroupRecord(read, header);
   return readGroup != null ? readGroup.getSample() : null;
 }
Exemple #4
0
 /**
  * Returns the platform unit associated with the provided read's read group.
  *
  * @param read read whose platform unit to retrieve
  * @param header SAM header containing read groups
  * @return the platform unit for the provided read's read group as a String, or null if the read
  *     has no read group.
  */
 public static String getPlatformUnit(final GATKRead read, final SAMFileHeader header) {
   final SAMReadGroupRecord readGroup = getSAMReadGroupRecord(read, header);
   return readGroup != null ? readGroup.getPlatformUnit() : null;
 }
  @Override
  public void execute() {
    log.info("Initializing kmer code map...");
    Map<Character, Integer> kmerCodeIndices = new HashMap<Character, Integer>();
    kmerCodeIndices.put('0', 1);
    kmerCodeIndices.put('A', 3);
    kmerCodeIndices.put('B', 4);
    kmerCodeIndices.put('C', 5);
    kmerCodeIndices.put('_', 6);
    kmerCodeIndices.put('.', 7);
    kmerCodeIndices.put('1', 9);

    Map<Character, String> kmerCodeNames = new LinkedHashMap<Character, String>();
    kmerCodeNames.put('0', "ref0");
    kmerCodeNames.put('A', "repetitive");
    kmerCodeNames.put('B', "both");
    kmerCodeNames.put('C', "lowcoverage");
    kmerCodeNames.put('_', "lowconfidence");
    kmerCodeNames.put('.', "novel");
    kmerCodeNames.put('1', "ref1");

    if (KMER_CODE_NAMES != null) {
      for (Character c : kmerCodeNames.keySet()) {
        String cStr = String.valueOf(c);
        if (KMER_CODE_NAMES.containsKey(cStr)) {
          kmerCodeNames.put(c, KMER_CODE_NAMES.get(cStr));
        }
      }
    }

    for (Character c : kmerCodeNames.keySet()) {
      log.info("  {} {}: {}", c, kmerCodeIndices.get(c), kmerCodeNames.get(c));
    }

    log.info("Loading annotated contigs...");
    Map<String, Map<String, String>> annotatedContigs = new HashMap<String, Map<String, String>>();
    int kmerSize = 0;

    if (ANN.length() > 0) {
      TableReader tr = new TableReader(ANN);
      for (Map<String, String> te : tr) {
        String contigName = te.get("contigName");

        if (kmerSize == 0) {
          kmerSize = te.get("seq").length() - te.get("kmerOrigin").length() + 1;
        }

        annotatedContigs.put(contigName, te);

        String[] ref0ToCanonicalExact =
            (te.get("ref0ToCanonicalExact").equals("NA")
                        || te.get("ref0ToCanonicalExact").equals("*:0-0")
                    ? "NA:0-0"
                    : te.get("ref0ToCanonicalExact"))
                .split("[:-]");
        String[] ref1ToCanonicalExact =
            (te.get("ref1ToCanonicalExact").equals("NA")
                        || te.get("ref1ToCanonicalExact").equals("*:0-0")
                    ? "NA:0-0"
                    : te.get("ref1ToCanonicalExact"))
                .split("[:-]");

        cout.println(
            te.get("sampleName")
                + "_"
                + te.get("accession")
                + "_"
                + contigName
                + " "
                + ref0ToCanonicalExact[0]
                + " "
                + ref0ToCanonicalExact[1]
                + " "
                + ref0ToCanonicalExact[2]
                + " radius1=0.8r");
        cout.println(
            te.get("sampleName")
                + "_"
                + te.get("accession")
                + "_"
                + contigName
                + " "
                + ref1ToCanonicalExact[0]
                + " "
                + ref1ToCanonicalExact[1]
                + " "
                + ref1ToCanonicalExact[2]
                + " radius2=0.6r");
      }
    }

    log.info("    contigs: {}", annotatedContigs.size());
    log.info("  kmer size: {}", kmerSize);

    log.info("Computing kmer inheritance information...");

    SAMFileHeader sfh = CONTIGS.getFileHeader();
    for (Character c : kmerCodeNames.keySet()) {
      SAMReadGroupRecord rgr = new SAMReadGroupRecord(kmerCodeNames.get(c));
      rgr.setSample(kmerCodeNames.get(c));
      sfh.addReadGroup(rgr);
    }

    SAMFileWriterFactory sfwf = new SAMFileWriterFactory();
    sfwf.setCreateIndex(true);
    SAMFileWriter sfw = sfwf.makeBAMWriter(sfh, false, bout);

    TableWriter tw = new TableWriter(sout);

    Set<IGVEntry> igvEntries = new TreeSet<IGVEntry>();
    int numContigs = 0;
    for (SAMRecord contig : CONTIGS) {
      if (CONTIG_NAMES == null
          || CONTIG_NAMES.isEmpty()
          || CONTIG_NAMES.contains(contig.getReadName())) {
        Map<String, String> te = annotatedContigs.get(contig.getReadName());

        if (annotatedContigs.containsKey(contig.getReadName())) {
          String seq = contig.getReadString();

          // log.debug("  te: {}", te);

          String annSeq = te.get("seq");
          String kmerOrigin = te.get("kmerOrigin");

          Map<CortexKmer, Character> kmerCodes = new HashMap<CortexKmer, Character>();
          for (int i = 0; i < kmerOrigin.length(); i++) {
            CortexKmer kmer = new CortexKmer(annSeq.substring(i, i + kmerSize));
            Character code = kmerOrigin.charAt(i);

            kmerCodes.put(kmer, code);
          }

          Map<Character, Integer> kmerStats = new HashMap<Character, Integer>();
          for (Character c : kmerCodeNames.keySet()) {
            kmerStats.put(c, 0);
          }

          boolean changed = false;

          // We want to be able to examine soft-clipped regions as well.
          List<CigarElement> ces = new ArrayList<CigarElement>();
          for (CigarElement ce : contig.getCigar().getCigarElements()) {
            if (ce.getOperator().equals(CigarOperator.S)) {
              ces.add(new CigarElement(ce.getLength(), CigarOperator.M));
              changed = true;
            } else {
              ces.add(ce);
            }
          }

          if (changed) {
            CigarElement firstCe = contig.getCigar().getCigarElements().get(0);

            if (firstCe.getOperator().equals(CigarOperator.S)) {
              contig.setAlignmentStart(contig.getAlignmentStart() - firstCe.getLength());
            }

            contig.setCigar(new Cigar(ces));
          }

          for (AlignmentBlock ab : contig.getAlignmentBlocks()) {
            for (int i = ab.getReadStart() - 1; i < ab.getReadStart() + ab.getLength(); i++) {
              if (i + kmerSize < seq.length()) {
                CortexKmer kmer = new CortexKmer(seq.substring(i, i + kmerSize));

                SAMRecord skmer = new SAMRecord(CONTIGS.getFileHeader());
                skmer.setReadBases(seq.substring(i, i + kmerSize).getBytes());

                List<CigarElement> cigarElements = new ArrayList<CigarElement>();
                cigarElements.add(new CigarElement(kmerSize, CigarOperator.M));
                Cigar cigar = new Cigar(cigarElements);

                skmer.setReadName(contig.getReadName() + "." + kmer.getKmerAsString());
                skmer.setReferenceName(contig.getReferenceName());
                skmer.setCigar(cigar);
                skmer.setReadPairedFlag(false);
                skmer.setDuplicateReadFlag(false);
                skmer.setMateNegativeStrandFlag(false);
                skmer.setAlignmentStart(ab.getReferenceStart() - ab.getReadStart() + 1 + i);
                skmer.setAttribute("RG", "none");
                skmer.setMappingQuality(0);

                Character c = kmerCodes.get(kmer);
                String codeName = kmerCodeNames.get(c);

                String parentReadGroupId = null;
                String sampleReadGroupId = null;
                for (SAMReadGroupRecord rgr : sfh.getReadGroups()) {
                  if (rgr.getSample().equals(codeName)) {
                    parentReadGroupId = rgr.getReadGroupId();
                  }

                  if (rgr.getSample().equals(contig.getReadGroup().getSample())) {
                    sampleReadGroupId = rgr.getReadGroupId();
                  }
                }

                skmer.setAttribute(
                    "RG", parentReadGroupId != null ? parentReadGroupId : sampleReadGroupId);
                skmer.setMappingQuality(99);

                sfw.addAlignment(skmer);

                kmerStats.put(c, kmerStats.get(c) + 1);

                IGVEntry igvEntry = new IGVEntry();
                igvEntry.chromosome = contig.getReferenceName();
                igvEntry.start = ab.getReferenceStart() - ab.getReadStart() + i;
                igvEntry.parentageName = kmerCodeNames.get(c);
                igvEntry.parentage = kmerCodeIndices.get(c);
                igvEntries.add(igvEntry);
              }
            }
          }

          if (!contig.isSecondaryOrSupplementary()) {
            beout.println(
                contig.getReferenceName()
                    + "\t"
                    + contig.getAlignmentStart()
                    + "\t"
                    + contig.getAlignmentEnd()
                    + "\t"
                    + contig.getReadName()
                    + "."
                    + contig.getReadGroup().getSample());

            if (annotatedContigs.size() > 10 && numContigs % (annotatedContigs.size() / 10) == 0) {
              log.info("  processed {}/{} contigs", numContigs, annotatedContigs.size());
            }
            numContigs++;
          }

          Map<String, String> stats = new LinkedHashMap<String, String>();
          stats.put("contigName", contig.getReadName());
          stats.put("sampleName", contig.getReadGroup().getSample());
          for (Character c : kmerCodeNames.keySet()) {
            stats.put(kmerCodeNames.get(c), String.valueOf(kmerStats.get(c)));
          }
          tw.addEntry(stats);
        }
      }
    }

    log.info("Writing kmer inheritance information...");
    out.printf("%s\t%s\t%s\t%s\t%s\n", "Chromosome", "Start", "End", "Feature", "Parentage");
    for (IGVEntry igvEntry : igvEntries) {
      out.printf(
          "%s\t%d\t%d\t%s\t%d\n",
          igvEntry.chromosome,
          igvEntry.start,
          igvEntry.start + 1,
          igvEntry.parentageName,
          igvEntry.parentage);
    }

    sfw.close();
  }