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 50
(instead of the default at 70) use clip_args="${clip_args} -s 50".
See the clip manual page (see section Clip) for full
details of the parameters available. Note that the clip program (as can all
the external programs used) can be replaced for any other program by
redefining the clip variable (eg clip=our_clip). The replacement
program will be called with the the clip_args specified and the name of the
Experiment File to clip. Clip programs that work on a trace file must read the
name of this trace file from the Experiment File.
In particular, to use trace_clip instead of clip simply add
clip="trace_clip" to the `.pregapc' file. The trace_clip
program (see section Trace_clip) performs the same task
as clip except uses the trace data instead of the called sequence. In
general it should do a better task, but needs setting up correctly before
hand. The scale_trace_clip program (see section Scale_trace_clip) can be used to derive some arguments for
trace_clip which should then be set using the clip_args
variable.
Startup parameters may also be specified for Trev. By default these
will be "-restrict -edits 0". Setting the trev_args variable
will override these defaults, but please make sure the default arguments are
still included. For example, to start trev at a specified position and size on
the screen with a slightly larger than normal magnification use
trev_args="${trev_args} -geometry 900x300+100+100 -xmag 200".See section Trev.
The vector_clip and repe programs used by Pregap require several
argument parameters to fine tune their searching algorithms. Generally these
do not need to be changed. Consult the vector_clip and repe
(see section Screening Against Vector Sequences)
documentation for full details on the meaning of
these questions. 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.
Note that these variables still start with vepe_. This is simply to
keep backwards compatibility. Pregap now uses vector_clip instead of
vepe, but still reads the vepe_ parameters.
--vector_clip -s: mark sequencing vector-- vepe_svec_word_length Word Length vepe_svec_diagonal Number of diagonals to combine vepe_svec_score Cutoff score vepe_svec_min_length Minimum length or percentage of vector. See vector_clip manual page --vector_clip -c: mark cloning vector-- vepe_cvec_word_length Word Length vepe_cvec_diagonal Number of diagonals to combine vepe_cvec_score Cutoff score --vector_clip -r: 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
Finally, it is sometimes useful to derive the experiment file name
and reading name from the ABI filename rather than the sample named
contained within it. This can now be done by answering the "Use ABI sample
names?" question, however the previous method of implementing this is still
instructive for people requiring yet another way of deriving their reading
names. Answering yes to the question simply executes the abi_filenames
command which redefines the abi_SCF_com, abi_Exp_com and
abi_Ent_com variables as follows.
abi_SCF_com='echo "${file}.scf"'
abi_Exp_com='echo "${file}.exp"'
abi_Ent_com='echo "${file}" | sed "s/ /_/g"'
If this has been made the default mode of operation, it can be switched back
by adding the use_sample_names=no command to the .pregaprc file.
To use a different filename derivation than used by abi_filenames
add use_sample_names=pregaprc and your own definitions of the above
three _com commands to the .pregaprc file.