[MAIN] Startup : x64 (DEBUG) (build Aug 30 2012 19:14:48)
Usage:  ngm [-c <path>] -q <reads> -r <reference> -o <output> [parameter]

Input/Output:

  -c/--config <path>            Path to the config file. The config file contains all advanced options.
                                If this parameter is omitted, default values will be used.
  -r/--reference <path>         Path to the reference genome (format: FASTA, can be gzipped).
  -q/--query <path>             Path to the read file. Valid input formats are: FASTA/Q (gzipped), SAM/BAM
                                If the query file is omitted, NGM will only preprocess the reference.
  -p/--paired                   Input data is paired end. (default: off)
  -I/--min-insert-size          The minimum insert size for paired end alignments (default: 0)
  -X/--max-insert-size          The maximum insert size for paired end alignments (default: 1000)

Output:

  -o/--output <path>            Path to output file.
  --hard-clip					Use hard instead of soft clipping for SAM output
  --silent-clip					Hard clip reads but don't add clipping information to CIGAR string

General:

  -t/--threads <int>            Number of candidate search threads
  -s/--sensitivity <float>      A value between 0 and 1 that determines the number of possible mapping
                                locations that will be evaluated with an sequence alignment.
                                0 means that all possible mapping locations will be evaluated
                                1 means that only the best possible mapping location(s) will be evaluated
                                Higher values will reduce the runtime but also have a negativ effect on maping sensitivity.
                                (default: estimated from input data)
  -i/--min-identity <0-1>       All reads mapped with an identity lower than this threshold will be reported as unmapped (default: 0.0)
  -R/--min-residues <int>         All reads mapped with lower than <int> residues will be reported as unmapped (default: 0.0)
  -g/--gpu [int,...]            Use GPU(s) for alignment computation (GPU Ids are zero-bassed!).
                                   With -g or --gpu GPU 0 will be used.
                                   With -g 1 or --gpu 1 GPU 1 will be used.
                                   With -g 0,1 or --gpu 0,1 GPU 0 and 1 will be used.
                                If -g/--gpu is ommitted, alignments will be computed on the CPU (not supported for bs-mapping!)
  --bs-mapping                  Enables bisulfite mapping (For bs-mapping kmer-skip will be applied to
                                the reads instead of the reference sequence).
  -h/--help                     Prints help and aborts program

Advanced settings:

  -k/--kmer [10-14]             Kmer length in bases. (default: 13)
  --kmer-skip <int>             Number of k-mers to skip when building the lookup table from
                                the reference(default: 2)
  -m/mode [0|1]                 Alignment mode: 0 = local, 1 = semi-global. (default: 0)
  --corridor <int>              Width of SW corridor (default: 15)