
The following parameters are available.  Ones with "[]" are in effect:

Input Parameters
 --in [testFiles/nonExistentFile.sam], --noeof,
               --refFile [testFilesLibBam/chr1_partial.fa], --maxErrors [-1],
               --verbose [ON], --printableErrors [100], --disableStatistics,
               --params [ON]
   SortOrder : --so_flag, --so_coord, --so_query

Failed opening the SAM/BAM file, returning: 3 (FAIL_IO)
FAIL_IO: Failed to Open testFiles/nonExistentFile.sam for reading
