check_assembly

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

The database IO handle returned from a previous open_db call.

-contigs identifiers

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.

-cutoff use_cutoffs

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.

-min_len min_length

-win_size window_length

-max_dashes count

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 -max_dashes.

-max_pmismatch percentage

Only matches with greater than the specified percentage mismatch are displayed as problems. The default is 15.0.