コード例 #1
0
ファイル: NWaySAMFileWriter.java プロジェクト: GinYan/gatk
  /**
   * Instantiates multiple underlying SAM writes, one per input SAM reader registered with GATK
   * engine (those will be retrieved from <code>toolkit</code>). The output file names will be
   * generated automatically by stripping ".sam" or ".bam" off the input file name and adding ext
   * instead (e.g. ".cleaned.bam"). onto a unique output file name.
   *
   * @param toolkit
   * @param ext
   */
  public void setupByReader(
      GenomeAnalysisEngine toolkit,
      String ext,
      SAMFileHeader.SortOrder order,
      boolean presorted,
      boolean indexOnTheFly,
      boolean generateMD5,
      SAMProgramRecord pRecord) {
    for (SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs()) {

      String fName = toolkit.getReadsDataSource().getSAMFile(rid).getName();

      String outName;
      int pos;
      if (fName.toUpperCase().endsWith(".BAM")) pos = fName.toUpperCase().lastIndexOf(".BAM");
      else {
        if (fName.toUpperCase().endsWith(".SAM")) pos = fName.toUpperCase().lastIndexOf(".SAM");
        else
          throw new UserException.BadInput(
              "Input file name " + fName + " does not end with .sam or .bam");
      }
      String prefix = fName.substring(0, pos);
      outName = prefix + ext;

      if (writerMap.containsKey(rid))
        throw new StingException(
            "nWayOut mode: Reader id for input sam file " + fName + " is already registered");
      addWriter(rid, outName, order, presorted, indexOnTheFly, generateMD5, pRecord);
    }
  }
コード例 #2
0
ファイル: NWaySAMFileWriter.java プロジェクト: GinYan/gatk
  /**
   * Instantiates multiple underlying SAM writes, one per input SAM reader registered with GATK
   * engine (those will be retrieved from <code>toolkit</code>). The <code>in2out</code> map must
   * contain an entry for each input filename and map it onto a unique output file name.
   *
   * @param toolkit
   * @param in2out
   */
  public void setupByReader(
      GenomeAnalysisEngine toolkit,
      Map<String, String> in2out,
      SAMFileHeader.SortOrder order,
      boolean presorted,
      boolean indexOnTheFly,
      boolean generateMD5,
      SAMProgramRecord pRecord) {
    if (in2out == null)
      throw new StingException("input-output bam filename map for n-way-out writing is NULL");
    for (SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs()) {

      String fName = toolkit.getReadsDataSource().getSAMFile(rid).getName();

      String outName;
      if (!in2out.containsKey(fName))
        throw new UserException.BadInput(
            "Input-output bam filename map does not contain an entry for the input file " + fName);
      outName = in2out.get(fName);

      if (writerMap.containsKey(rid))
        throw new StingException(
            "nWayOut mode: Reader id for input sam file "
                + fName
                + " is already registered; "
                + "map file likely contains multiple entries for this input file");

      addWriter(rid, outName, order, presorted, indexOnTheFly, generateMD5, pRecord);
    }
  }
コード例 #3
0
ファイル: NWaySAMFileWriter.java プロジェクト: GinYan/gatk
 public void addAlignment(SAMRecord samRecord) {
   final SAMReaderID id = toolkit.getReaderIDForRead(samRecord);
   String rg = samRecord.getStringAttribute("RG");
   if (rg != null) {
     String rg_orig = toolkit.getReadsDataSource().getOriginalReadGroupId(rg);
     samRecord.setAttribute("RG", rg_orig);
   }
   addAlignment(samRecord, id);
 }