Esempio n. 1
0
 private void echo(FastqWriter fqw, MappedFastq rec) {
   fqw.write(
       new FastqRecord(
           rec.name + " " + ((int) rec.side) + ":N:0:1", rec.seq, new String(""), rec.qual));
 }
Esempio n. 2
0
  @Override
  public int doWork(String[] args) {
    boolean repair_missing_read = false;
    SortingCollectionFactory<MappedFastq> sortingFactory =
        new SortingCollectionFactory<MappedFastq>();
    File forwardFile = null;
    File reverseFile = null;
    com.github.lindenb.jvarkit.util.cli.GetOpt opt =
        new com.github.lindenb.jvarkit.util.cli.GetOpt();
    int c;

    sortingFactory.setComponentType(MappedFastq.class);
    sortingFactory.setCodec(new MappedFastqCodec());
    sortingFactory.setComparator(new MappedFastqComparator());

    while ((c = opt.getopt(args, super.getGetOptDefault() + "F:R:N:r")) != -1) {
      switch (c) {
        case 'F':
          forwardFile = new File(opt.getOptArg());
          break;
        case 'R':
          reverseFile = new File(opt.getOptArg());
          break;
        case 't':
          addTmpDirectory(new File(opt.getOptArg()));
          break;
        case 'N':
          sortingFactory.setMaxRecordsInRAM(Math.max(Integer.parseInt(opt.getOptArg()), 100));
          break;
        case 'r':
          repair_missing_read = true;
          break;
        case ':':
          System.err.println("Missing argument for option -" + opt.getOptOpt());
          return -1;
        default:
          {
            switch (handleOtherOptions(c, opt, args)) {
              case EXIT_FAILURE:
                return -1;
              case EXIT_SUCCESS:
                return 0;
              default:
                break;
            }
          }
      }
    }
    SAMFileReader sfr = null;
    SortingCollection<MappedFastq> fastqCollection = null;
    try {
      sortingFactory.setTmpDirs(this.getTmpDirectories());
      fastqCollection = sortingFactory.make();
      fastqCollection.setDestructiveIteration(true);
      boolean found_single = false;
      boolean found_paired = false;
      long non_primary_alignmaned_flag = 0L;

      if (opt.getOptInd() == args.length) {
        info("Reading from stdin");
        sfr = new SAMFileReader(System.in);
      } else if (opt.getOptInd() + 1 == args.length) {
        String filename = args[opt.getOptInd()];
        sfr = new SAMFileReader(new File(filename));
      } else {
        error(getMessageBundle("illegal.number.of.arguments"));
        return -1;
      }
      sfr.setValidationStringency(ValidationStringency.LENIENT);
      SAMRecordIterator iter = sfr.iterator();
      SAMSequenceDictionaryProgress progress =
          new SAMSequenceDictionaryProgress(sfr.getFileHeader().getSequenceDictionary());
      while (iter.hasNext()) {
        SAMRecord rec = iter.next();
        progress.watch(rec);

        if (rec.isSecondaryOrSupplementary()) {
          if (non_primary_alignmaned_flag == 0) {
            warning("SKIPPING NON-PRIMARY " + (non_primary_alignmaned_flag + 1) + " ALIGNMENTS");
          }
          non_primary_alignmaned_flag++;
          continue;
        }

        MappedFastq m = new MappedFastq();
        m.name = rec.getReadName();
        if (m.name == null) m.name = "";
        m.hash = m.name.hashCode();
        m.seq = rec.getReadString();

        if (m.seq.equals(SAMRecord.NULL_SEQUENCE_STRING)) m.seq = "";
        m.qual = rec.getBaseQualityString();
        if (m.qual.equals(SAMRecord.NULL_QUALS_STRING)) m.qual = "";
        if (!rec.getReadUnmappedFlag() && rec.getReadNegativeStrandFlag()) {
          m.seq = AcidNucleics.reverseComplement(m.seq);
          m.qual = new StringBuilder(m.qual).reverse().toString();
        }
        if (m.seq.length() != m.qual.length()) {
          error("length(seq)!=length(qual) in " + m.name);
          continue;
        }
        if (m.seq.isEmpty() && m.qual.isEmpty()) {
          m.seq = "N";
          m.qual = "#";
        }

        if (rec.getReadPairedFlag()) {
          found_paired = true;
          if (found_single) {
            sfr.close();
            throw new PicardException("input is a mix of paired/singled reads");
          }
          m.side = (byte) (rec.getSecondOfPairFlag() ? 2 : 1);
        } else {
          found_single = true;
          if (found_paired) {
            sfr.close();
            throw new PicardException("input is a mix of paired/singled reads");
          }
          m.side = (byte) 0;
        }
        fastqCollection.add(m);
      }
      iter.close();
      CloserUtil.close(iter);
      CloserUtil.close(sfr);
      progress.finish();

      fastqCollection.doneAdding();
      info("Done reading.");

      if (found_paired) {
        FastqWriter fqw1 = null;
        FastqWriter fqw2 = null;
        if (forwardFile != null) {
          info("Writing to " + forwardFile);
          fqw1 = new BasicFastqWriter(forwardFile);
        } else {
          info("Writing to stdout");
          fqw1 = new BasicFastqWriter(new PrintStream(System.out));
        }
        if (reverseFile != null) {
          info("Writing to " + reverseFile);
          fqw2 = new BasicFastqWriter(reverseFile);
        } else {
          info("Writing to interlaced stdout");
          fqw2 = fqw1;
        }
        List<MappedFastq> row = new ArrayList<MappedFastq>();
        CloseableIterator<MappedFastq> r = fastqCollection.iterator();
        for (; ; ) {
          MappedFastq curr = null;
          if (r.hasNext()) curr = r.next();
          if (curr == null || (!row.isEmpty() && !row.get(0).name.equals(curr.name))) {
            if (!row.isEmpty()) {
              if (row.size() > 2) {
                warning("WTF :" + row);
              }
              boolean found_F = false;
              boolean found_R = false;
              for (MappedFastq m : row) {
                switch ((int) m.side) {
                  case 1:
                    if (found_F)
                      throw new PicardException("two forward reads found for " + row.get(0).name);
                    found_F = true;
                    echo(fqw1, m);
                    break;
                  case 2:
                    if (found_R)
                      throw new PicardException("two reverse reads found for " + row.get(0).name);
                    found_R = true;
                    echo(fqw2, m);
                    break;
                  default:
                    throw new IllegalStateException("uh???");
                }
              }
              if (!found_F) {
                if (repair_missing_read) {
                  warning("forward not found for " + row.get(0));
                  MappedFastq pad = new MappedFastq();
                  pad.side = (byte) 1;
                  pad.name = row.get(0).name;
                  pad.seq = "N";
                  pad.qual = "#";
                  echo(fqw1, pad);
                } else {
                  throw new PicardException("forward not found for " + row);
                }
              }
              if (!found_R) {
                if (repair_missing_read) {
                  warning("reverse not found for " + row.get(0));
                  MappedFastq pad = new MappedFastq();
                  pad.side = (byte) 2;
                  pad.name = row.get(0).name;
                  pad.seq = "N";
                  pad.qual = "#";
                  echo(fqw2, pad);
                } else {
                  throw new PicardException("reverse not found for " + row);
                }
              }
            }
            if (curr == null) break;
            row.clear();
          }
          row.add(curr);
        }
        r.close();
        fqw1.close();
        fqw2.close();
      } else if (found_single) {
        FastqWriter fqw1 = null;
        if (forwardFile != null) {
          info("Writing to " + forwardFile);
          fqw1 = new BasicFastqWriter(forwardFile);
        } else {
          info("Writing to stdout");
          fqw1 = new BasicFastqWriter(new PrintStream(System.out));
        }

        CloseableIterator<MappedFastq> r = fastqCollection.iterator();
        while (r.hasNext()) {
          echo(fqw1, r.next());
        }
        r.close();
        fqw1.close();
      }
      return 0;
    } catch (Exception err) {
      error(err);
      return -1;
    } finally {
      if (fastqCollection != null) fastqCollection.cleanup();
    }
  }