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.
The database IO handle returned from a previous
This specifies the list of contigs to check. Only the contig identifier is
currently used, although the syntax specifying start and end ranges is valid.
Controls whether the cutoff data is to be analysed. If use_cutoffs is a
non zero value the cutoff data will be aligned and compared against the
consensus. Otherwise the already aligned used data will be compared against
the consensus. The default is 1.
These parameters are only used when -cutoff is enabled. The criteria for
determining how much cutoff sequence to align is selected as only the portion
where no more than count unknown ("-") bases within a region of
window_length bases. This sequence is then only used if the amount
selected is at least min_length bases long. The defaults are 10 for
-min_len, 29 for
-win_size and 3 for
Only matches with greater than the specified percentage mismatch are displayed
as problems. The default is 15.0.
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Last generated on 1 March 2001.