Package net.sf.picard.reference

Examples of net.sf.picard.reference.ReferenceSequenceFile

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    }
    return null;
  }

  public static ReferenceSequenceFile findReferenceSequenceFileOrFail(Object... sources) {
    ReferenceSequenceFile referenceSequenceFile = null;

    if (sources != null)
      for (Object source : sources) {
        if (source == null)
          continue;
        ReferenceSequenceFile foundFile = referenceFactory.get(source);
        if (foundFile != null)
          return foundFile;

        // last resort, using a blind-walk method in a black room to
        // find a
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            else bufferedStream = IOUtil.toBufferedStream(stream);
            if (isCRAMFile(bufferedStream)) {
                mIsBinary = true;
        if (file != null && file.isFile())
          bufferedStream.close();
        ReferenceSequenceFile referenceSequenceFile = ReferenceDiscovery
            .findReferenceSequenceFileOrFail(stream, file,
                indexFile);
        if (indexFile != null && file != null)
          mReader = new CRAMFileReader (file, indexFile, referenceSequenceFile) ;
        else
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Related Classes of net.sf.picard.reference.ReferenceSequenceFile

  • net.sf.cram.Bam2Cram
  • net.sf.cram.BLOCK_PROTO
  • net.sf.cram.Coder
  • net.sf.cram.Cram2Bam
  • net.sf.cram.Merge
  • net.sf.cram.SpotAssemblyTest
  • net.sf.cram.Utils
  • net.sf.cram.ValidateCramFile
  • net.sf.samtools.ReferenceDiscovery
  • net.sf.samtools.SAMFileReader
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