NAME
gt-chain2dim - Chain pairwise matches.
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 
REPORTING BUGS
Report bugs to <kurtz@zbh.uni-hamburg.de>.