SYNOPSIS
gt chain2dim [options] -m matchfile
DESCRIPTION
-m [filename]
- Specify file containing the matches mandatory option (default: undefined)
-global
-
perform global chaining
- • optional parameter gc switches on gap costs (according to L1-model)
- • optional parameter ov means that overlaps between matches are allowed
- • optional parameter all means that all optimal chains are processed
-local
-
perform local chaining compute local chains (according to L1-model).
- • If no parameter is given, compute local chains with maximums score.
- • If parameter is given, this must be a positive number optionally followed by the character b or p.
- • If only the number, say k, is given, this is the minimum score of the chains output.
- • If a number is followed by character b, then output all chains with the largest k scores.
- • If a number is followed by character p, then output all chains with scores at most k percent away from the best score.
-wf [value]
- specify weight factor > 0.0 to obtain score of a fragment requires one of the options -local const -global gc -global ov (default: 1.000000)
-maxgap [value]
- specify maximal width of gap in chain (default: 0)
-silent [yes|no]
- do not output the chains but only report their lengths and scores (default: no)
-v [yes|no]
- be verbose (default: no)
-help
- display help and exit
-version
- display version information and exit