# list of files of the initial bas.h5 files 
input_fofn = input.fofn 
#input_fofn = preads.fofn 

input_type = raw 
#input_type = preads 

# The length cutoff used for seed reads used for initial mapping 
length_cutoff = 8000 

# The length cutoff used for seed reads used for pre-assembly 
length_cutoff_pr = 12000 

# Cluster queue setting 
jobqueue = pacmanqueue1 
sge_option_da = -pe smp 8 -q %(jobqueue)s 
sge_option_la = -pe smp 4 -q %(jobqueue)s 
sge_option_pda = -pe smp 8 -q %(jobqueue)s 
sge_option_pla = -pe smp 4 -q %(jobqueue)s 
sge_option_fc = -pe smp 16 -q %(jobqueue)s 
sge_option_cns = -pe smp 4 -q %(jobqueue)s 

pa_concurrent_jobs = 12 
cns_concurrent_jobs = 24 
ovlp_concurrent_jobs = 12 

pa_HPCdaligner_option = -v -dal128 -t16 -e.70 -l1000 -s1000 
ovlp_HPCdaligner_option = -v -dal128 -t32 -h60 -e.96 -l500 -s1000 

pa_DBsplit_option = -x500 -s400 
ovlp_DBsplit_option = -x500 -s400 

falcon_sense_option = --output_multi --min_idt 0.70 --min_cov 4 --local_match_count_threshold 2 --max_n_read 200 --n_core 8 --output_dformat 

overlap_filtering_setting = --max_diff 100 --max_cov 100 --min_cov 1 --bestn 10 --n_core 8