find_internal_joins
-io io_handle:integer
-contigs identifiers:strings
?-mode mode:string(end_all)?
?-segment identifier:string()?
?-min_match length:integer(15)?
?-max_pads count:integer(25)?
?-max_pmismatch percentage:float(30.0)?
?-win_size length:integer(0)?
?-max_dashes count:integer(0)?
?-probe_length length:integer(100)?
?-mask mask:string(none)?
?-tag_types types:string()?
This command searches for potential joins between contigs by comparing the sequence data in each contig. This information is plotted on the Contig Selector. The command will not work if the Contig Selector is not displayed. The function returns no value but will generate a Tcl error if an error occurs.
-io
io_handle
open_db
call.
-contigs
identifiers
-mode
mode
end_end
end_all
all_all
segment
end_all
".
-segment
identifier
segment
" this specifies the region of the contig
identifier to compare. The default is blank.
-min_match
length
-max_pads
count
-max_pmismatch
count
-win_size
length
-max_dashes
count
-mask
mask
-tag_types
mask
mark
" the sequence is converted to an alternative
character set so that matches will be found, but are clearly visible in the
output as being matches between marked fragments. When mask is
"mask
" the sequence is removed so that no matches will be initiated
between this sequence and another fragment. The defaults are"
none
" for mask and a blank string for the tag types, which
disables masking and marking.