defaults.txt

#default config file
#any new category must have a "category" feature (which can correspond to the categoty's name)
#white line define breaks between categories
#singe feature should be added under the general category above.
#general default parameters
category=general
type=normal
DNA.BAM.files=cool
sensitivity=25
cores=5

#specific paramenters
#species
category=species
species=arabidopsis
organism_type=plants
genome_index=undefined
STAR_intron_max=10000
STAR_mates_gap=10000
STAR_params=
species=human
organism_type=mammals
genome_index=undefined
STAR_intron_max=100000
STAR_mates_gap=100000
STAR_params=
species=None
organism_type=bacteria
genome_index=undefined
STAR_intron_max=1
STAR_mates_gap=1000
STAR_params=
species=trichinella
organism_type=nematoda
genome_index=undefined
STAR_intron_max=1000
STAR_mates_gap=1000
STAR_params=

#material
category=material
material=DNA
gap_open_penality=2
mm_penality=1
material=RNA
gap_open_penality=3
mm_penality=2