find_internal_joins

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

The database IO handle returned from a previous open_db call.

-contigs identifiers

This specifies the list of contigs to search. The {contig start end} syntax may be used for an identifier to search only a region of the contig, otherwise all of it is searched.

-mode mode

This specifies the segments of contigs in which to search for joins. Valid modes are:

end_end

Compares only the ends of each contigs with the ends of other contigs.

end_all

Compares the ends of each contigs with the entirety of other contigs.

all_all

Compares all of each contig with all of the other contigs.

segment

Compares a segment of a particular contig with all of the contig contigs.

The default mode is "end_all".

-segment identifier

When mode is "segment" this specifies the region of the contig identifier to compare. The default is blank.

-min_match length

Specifies the minimum length of exact match used during the hashing stage of find internal joins. The minium allowed value for this is 14. The default is 15.

-max_pads count

After alignments the number of pads required in each of the two consensus sequences must be less than or equal to count. The default is 25.

-max_pmismatch count

After alignments the percentage of bases that do not match must be less than or equal to percentage. This is a floating point value. The default is 30.0.

-win_size length

-max_dashes count

If these are both set to non-zero values the cutoff data will be searched for matches. The criteria for determining how much cutoff sequence to align is selected as the portion where no more than count unknown ("-") bases within a region of length bases. The defaults are 0 for both, which implies only used data should be searched.

-mask mask

-tag_types mask

If types is a non blank list of tag types then masking or marking will be applied to the sequence covered by tags of these types from. When mask is "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.