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Command Line Arguments

-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!).

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Last generated on 25 November 2011.