short flag,argument mask,data type,variable name
o,1,character,report
d,1,character,report.files_path
A,1,character,alignment_files
B,1,character,sample_names
G,1,character,gff
f,1,character,format
r,1,character,order
S,1,character,stranded
a,1,character,minaqual
T,1,character,feature_type
i,1,character,idattr
m,1,character,mode
c,1,character,count