-bitsize
-
Specifies whether the database file size is 32-bit or
64-bit. Practically speaking due to the use of signed numbers in
places and the restriction of 32-bit for the number of records in a
database (even when using
-bitsize 64
for 64-bit file offsets)
the practical limits are 2Gb filesize for -bitsize 32
and
somewhere around about 100-million sequences for -bitsize 64
.
Gap4 only needs this option for creating new databases. The bit-size
of existing databases is automatically detected when they are opened.
Databases produced in 64-bit format are not compatible with older
versions of Gap4, but old and newly created 32-bit databases still work with
the 64-bit Gap4 (and are maintained in 32-bit format so editing them
will not invalidate their use by older Gap4s). The copy_db
program (see section Copy_db) can be used to
convert file formats.
-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.
-check
-
-no_check
-
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.
-exec_notes
-
-no_exec_notes
-
Controls whether to search for and execute any Notes of type
OPEN
or CLOS
. This may be an important security measure
if you are using foreign databases. Gap4 defaults to -no_check_notes.
-rawdata_note
-
-no_rawdata_note
-
Controls whether to make use of the
RAWD
note type for
specifying the trace file search path. Defaults to -rawdata_note.
-csel
-
-no_csel
-
Controls whether to automatically start up the contig selector when
opening a new gap4 database. In some cases (such as when dealing with
many EST clusters each in their own contig) the contig selector is not
a practical tool; this simply offers a way of speeding up database
opening. Defaults to -csel.
--
-
Treat this as the last command line option. Only useful if the database name
is specified and the name starts with a minus character (not
recommended!).
Last generated on 25 November 2011.