Chain pairwise matches.
gt chain2dim [options] -m matchfile
-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
Report bugs to <[email protected]>.