Command_Line_Options

Command Line Options

 Usage: CloudBurst refpath qrypath outpath readlen k allowdifferences filteralignments #mappers #reduces #fmappers #freducers blocksize redundancy

 refpath:          path in hdfs to the reference file
 qrypath:          path in hdfs to the query file
 outpath:          path to a directory to store the results (old results are automatically deleted)
 readlen:          minimum length of the reads
 k:                number of mismatches / differences to allow (higher number requires more time)
 allowdifferences: 0: mismatches only, 1: indels as well 
 filteralignments: 0: all alignments, 1: only report unambiguous best alignment (results identical to RMAP)
 #mappers:         number of mappers to use.              suggested: #processor-cores * 10
 #reduces:         number of reducers to use.             suggested: #processor-cores * 2
 #fmappers:        number of mappers for filtration alg.  suggested: #processor-cores
 #freducers:       number of reducers for filtration alg. suggested: #processor-cores
 blocksize:        number of qry and ref tuples to consider at a time in the reduce phase. suggested: 128 
 redundancy:       number of copies of low complexity seeds to use. suggested: # processor cores