Examples of net.sf.samtools.SAMException

            "CRAM index is not compatible with BAM files.");


      SAMFileReader reader = new SAMFileReader(params.inputFile);
      if (!reader.isBinary()) {
        reader.close();
        throw new SAMException(
            "Input file must be bam file, not sam file.");
      }


      if (!reader.getFileHeader().getSortOrder()
          .equals(SAMFileHeader.SortOrder.coordinate)) {
        reader.close();
        throw new SAMException(
            "Input bam file must be sorted by coordinates");
      }


      File indexFile = new File(params.inputFile.getAbsolutePath()
          + ".bai");

      buf.putInt(array.length);
      for (final float element : array)
        buf.putFloat(element);


    } else
      throw new SAMException("Unrecognized array value type: "
          + value.getClass());
  }

Related Classes of net.sf.samtools.SAMException

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