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Command Line Arguments

check
nocheck
Specifies whether to run the "Check Database" option when opening new databases. -check forces this to always be done and -nocheck forces it to never be done. By default Check Database is always performed when opening databases in read-write mode and never performed when opening in read-only mode.

-maxdb
Specifies the maximum number of readings plus contigs. This value is not automatically adjusted whilst the program is running, but is not allowed to be set to a value too small for the database to be opened. It controls the size of some areas of memory (approximately 16*maxdb bytes) used during execution of Gap. The default value is 8000.

-maxseq
Specifies the maximum number of characters used in the concatenated consensus sequences. This parameter is generally not required as the value is normally computed and adjusted automatically. However a few functions (such as assembly) still need to know a maximum size before hand. The default is 100000 bases.

-ro
-read_only
Opens the database (if specified on the command line) in read only mode. This does not apply to databases opened using the file browser.

-no_exec_notes
Does not search for and execute any Notes of type OPEN or CLOS.

-no_rawdata_note
Does not make use of the RAWD note type for specifying the trace file search path.

--
Treat this as the last command line option. Only useful if the database name is specified and this database starts with a minus character (not recommended).

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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_2.html