GS Reference Mapper Command Line Interface

2. GS Reference Mapper : 2.15 GS Reference Mapper Command Line Interface

2.15	GS Reference Mapper Command Line Interface

2.15.1 Working with Project Folders and Data Files

2.15.2 One-Step Mapping: the runMapping Command

2.15.3 Incremental Mapping: the newMapping and Related Commands

The GS Reference Mapper CLI command for single shot mapping of reads can be launched using the following command:

runMapping [options] refdesc [filedesc]

For incremental mapping via the CLI, a project directory structure is created to organize the files of the incremental build of the project data. The following commands are used for incremental mapping projects:

newMapping projdir

addRun [options: -p, -lib, -mcf] [projdir] filedesc

removeRun [projdir] filedesc

setRef [options: -gref, -cref, -random] [projdir] refdesc

runProject [options] [projdir]

For all of these commands;

•	The arguments in brackets [ ] are optional.

•	‘options’ refers to the specific command options available.

•	‘filedesc’ is one of the following:

•	an sfffilename

•	a [regionlist:]datadir

•	a readfastafile

•

any of the above prepended by an [MIDList@] specification where each “MIDList” is a multiplexing information string used to filter the set of file reads to be used in the mapping (If MIDs were used in the generation of the read data file, then an MIDList string must be specified in order for the mapper to properly handle the file’s reads.) For details about using MIDs, see section 4.7.

•	‘refdesc’ is a path/name to a reference sequence file in FASTA format.

•	‘projdir’ is the path of the data analysis project directory.

Some of the command line options for Mapping are mutually exclusive, for obvious functional reasons. See section 4.5 for a list of these options.