Exemple #1
0
  /**
   * Create a common SAMFileWriter from a factory for use with GATK tools. Assumes that if the
   * factory has been set to create an index, the header must be set to coordinate sorted.
   *
   * @param outputFile if this file has a .cram extension then a reference is required. Can not be
   *     null.
   * @param referenceFile the reference source to use. Can not be null if a output file has a .cram
   *     extension.
   * @param header header to be used for the output writer
   * @param preSorted if true then records must already be sorted to match the header sort order
   * @param factory SAMFileWriterFactory factory to use
   * @return SAMFileWriter
   */
  public static SAMFileWriter createCommonSAMWriterFromFactory(
      final SAMFileWriterFactory factory,
      final File outputFile,
      final File referenceFile,
      final SAMFileHeader header,
      final boolean preSorted) {
    Utils.nonNull(outputFile);
    Utils.nonNull(header);

    if (null == referenceFile && outputFile.getName().endsWith(CramIO.CRAM_FILE_EXTENSION)) {
      throw new UserException("A reference file is required for writing CRAM files");
    }

    return factory.makeWriter(header.clone(), preSorted, outputFile, referenceFile);
  }
Exemple #2
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  @Override
  public int doWork(String[] args) {
    boolean compressed = false;
    int maxRecordsInRAM = 100000;
    long count = -1L;
    File fileout = null;
    com.github.lindenb.jvarkit.util.cli.GetOpt opt =
        new com.github.lindenb.jvarkit.util.cli.GetOpt();
    int c;
    while ((c = opt.getopt(args, getGetOptDefault() + "o:n:N:T:b")) != -1) {
      switch (c) {
        case 'b':
          compressed = true;
          break;
        case 'N':
          maxRecordsInRAM = Integer.parseInt(opt.getOptArg());
          break;
        case 'n':
          count = Long.parseLong(opt.getOptArg());
          break;
        case 'o':
          fileout = new File(opt.getOptArg());
          break;
        case 'T':
          this.addTmpDirectory(new File(opt.getOptArg()));
          break;
        default:
          {
            switch (handleOtherOptions(c, opt, null)) {
              case EXIT_FAILURE:
                return -1;
              case EXIT_SUCCESS:
                return 0;
              default:
                break;
            }
          }
      }
    }
    if (count < -1L) // -1 == infinite
    {
      error("Bad count:" + count);
      return -1;
    }
    SamReader samReader = null;
    SAMRecordIterator iter = null;
    SAMFileWriter samWriter = null;
    Random random = new Random();
    CloseableIterator<RandSamRecord> iter2 = null;
    try {
      SamFileReaderFactory.setDefaultValidationStringency(ValidationStringency.SILENT);
      if (opt.getOptInd() == args.length) {
        info("Reading from stdin");
        samReader = SamFileReaderFactory.mewInstance().openStdin();
      } else if (opt.getOptInd() + 1 == args.length) {
        File filename = new File(args[opt.getOptInd()]);
        info("Reading from " + filename);
        samReader = SamFileReaderFactory.mewInstance().open(filename);
      } else {
        error("Illegal number of arguments.");
        return -1;
      }
      SAMFileHeader header = samReader.getFileHeader();

      header = header.clone();
      header.setSortOrder(SortOrder.unsorted);
      header.addComment("Processed with " + getProgramName() + " : " + getProgramCommandLine());
      SAMFileWriterFactory sfw = new SAMFileWriterFactory();
      sfw.setCreateIndex(false);
      sfw.setCreateMd5File(false);
      if (fileout == null) {
        if (compressed) {
          samWriter = sfw.makeBAMWriter(header, true, System.out);
        } else {
          samWriter = sfw.makeSAMWriter(header, true, System.out);
        }
      } else {
        samWriter = sfw.makeSAMOrBAMWriter(header, true, fileout);
        this.addTmpDirectory(fileout);
      }
      iter = samReader.iterator();
      SAMSequenceDictionaryProgress progress =
          new SAMSequenceDictionaryProgress(samReader.getFileHeader().getSequenceDictionary());

      SortingCollection<RandSamRecord> sorter =
          SortingCollection.newInstance(
              RandSamRecord.class,
              new RandSamRecordCodec(header),
              new RandSamRecordComparator(),
              maxRecordsInRAM,
              getTmpDirectories());
      sorter.setDestructiveIteration(true);
      while (iter.hasNext()) {
        RandSamRecord r = new RandSamRecord();
        r.rand_index = random.nextInt();
        r.samRecord = progress.watch(iter.next());

        sorter.add(r);
      }
      iter.close();
      iter = null;

      sorter.doneAdding();
      iter2 = sorter.iterator();
      if (count == -1) {
        while (iter2.hasNext()) {
          samWriter.addAlignment(iter2.next().samRecord);
        }
      } else {
        while (iter2.hasNext() && count > 0) {
          samWriter.addAlignment(iter2.next().samRecord);
          count--;
        }
      }
      iter2.close();
      iter2 = null;
      sorter.cleanup();
      progress.finish();
    } catch (Exception e) {
      error(e);
      return -1;
    } finally {
      CloserUtil.close(iter);
      CloserUtil.close(iter2);
      CloserUtil.close(samReader);
      CloserUtil.close(samWriter);
    }
    return 0;
  }
Exemple #3
0
 /**
  * HACK: This is used to make a copy of a header. Really, SAMFileHeader should provide a copy
  * constructor or a factory method.
  */
 public static SAMFileHeader cloneSAMFileHeader(final SAMFileHeader header) {
   if (header == null) return null;
   return header.clone();
 }