CSC

assemble_direct

assemble_direct
 -io            io_handle:integer
 -files         filenames:strings
?-output_mode   mode:integer(0)?
?-max_pmismatch percentage:float(-1)?

This performs the gap4 directed assembly function. It takes a list of Experiment File filenames and processes these according to their content. The Experiment Files should contain AP lines to govern their positions in the assembly.

The function returns a list of failed files separated by newlines.

-io io_handle

The database IO handle returned from a previous open_db call.

-files filenames

A Tcl list of Experiment File filenames.

-output_mode mode

Whether to display alignments when assembling sequences containing a tolerance of zero or more. A mode of non-zero displays alignments, 0 does not. This is an optional argument with the default as 0.

-max_pmismatch percentage

When aligning sequences (tolerance >= 0) the aligned sequences must match the consensus sequence with <= percentage mismatch. A percentage of -1 implies no check should be made. The default for this option is -1.