Provided by: gasic_0.0.r19-5_amd64
run_mappers - run a read mapper to map reads to reference genomes
run_mappers NAMES READS -i REF -o OUT -m MAPPER
Run a read mapper to map reads to reference genomes. The names in the NAMES file will be inserted in the provided string patterns. Each pattern must contain exactly one "%s" placeholder (python string formatting).
NAMES Filename of the names file; the plain text names file should contain one name per line. The name is used as identifier in the whole algorithm. READS File containing the reads to be mapped. -h, --help show this help message and exit -m MAPPER, --mapper=MAPPER Identifier of mapper defined in core/tools.py [default: none] -i REF, --index=REF Pattern, that points to the reference sequences/indices when used with a name. Placeholder for the name is "%s". [default: ./ref/%s.fasta] -o OUT, --output=OUT Pattern, that points to the output SAM file, when used with a name. Placeholder for the name is "%s". [default: ./SAM/%s.sam]