Pregap can be further tuned by adding extra configuration parameters in the .pregaprc file. Common changes include changing the arguments to the external programs used and changing how pregap obtains the reading name from a file. The following section ( See section Integration with External Databases.) describes the SCF and Experiment File filename generation and the entry name calculations.
To configure the clip program to clip using different parameters set
the clip_args variable. To request clipping starting from base 40
(instead of the default at 20) use clip_args="-s 40". See the
clip manual page (see section Clip) for full details of
the parameters available. Note that the clip program (as can all the external
programs used) can be replaced for any other program by redefining the
clip variable (eg clip=our_clip). The replacement program will
be called with the the clip_args specified and the name of the Experiment File
to clip. Clip programs that work on a trace file must read the name of this
trace file from the Experiment File.
In particular, to use trace_clip instead of clip simply add
clip="trace_clip" to the `.pregapc' file. The trace_clip
program (see section Trace_clip) performs the same task
as clip except uses the trace data instead of the called sequence. In
general it should do a better task, but needs setting up correctly before
hand. The scale_trace_clip program (see section Scale_trace_clip) can be used to derive some arguments for
trace_clip which should then be set using the clip_args
variable.
Startup parameters may also be specified for Trev. By default these
will be "-restrict -edits 0". Setting the trev_args variable
will override these defaults, but please make sure the default arguments are
still included. For example, to start trev at a specified position and size on
the screen with a slightly larger than normal magnification use
trev_args="${trev_args} -geometry 900x300+100+100 -xmag 200".
See section `Trev' in trev.
The vepe and repe programs used by Pregap require several
arguments parameters to fine tune their searching algorithms. Generally these
do not need to be changed. Consult the vepe documentation for full details on
the meaning of these questions (see section Vepe introduction).
To see the answers to these questions used by pregap look at the
system-pregaprc file. A brief table of the questions and pregap variables
follows.
--Vepe option 1: mark sequencing vector-- vepe_svec_word_length Word Length vepe_svec_diagonal Number of diagonals to combine vepe_svec_score Cutoff score --Vepe option 2: mark cloning vector-- vepe_cvec_word_length Word Length vepe_cvec_diagonal Number of diagonals to combine vepe_cvec_score Cutoff score --Vepe option 3: check for vector rearrangements-- vepe_avec_min_match Minimum match length --Repe-- repe_repeat_file Input file of repeat file names repe_score Cutoff score repe_tag_type Four letter tag type