check_assembly
-io io_handle:integer
-contigs identifiers:strings
?-cutoff use_cutoffs:integer(1)?
?-min_len length:integer(10)?
?-win_size length:integer(29)?
?-max_dashes count:integer(3)?
?-max_pmismatch percentage:float(15.0)?
The command performs the Gap4 Check Assembly command. It compares either the used data or the cutoff data against the consensus sequence to find readings with poor match. The function is not currently ideally suitable for use in a script as it plots directly to the Contig Selector display. The function returns no value but will generate a Tcl error if an error occurs.
-io
io_handle
open_db
call.
-contigs
identifiers
-cutoff
use_cutoffs
-min_len
min_length
-win_size
window_length
-max_dashes
count
-min_len
, 29 for -win_size
and 3 for -max_dashes
.
-max_pmismatch
percentage