Stop all alignment filtering

[pre-mRNA]

Hi,

Thanks for making this package. It's extremely useful and easy to use. Great tool for the long read community!

I was wondering if there's a simple command to prevent any alignment filtering? I have played with all the flags in Counterr but approx ~20% of my alignments still 'fail' and are not considered in the analysis. Here are the flags I use:

-verbose -len_min_contig 5 -mapq_thres 0 -len_min_read 0 -len_min_aln 1 -bitflag 0 -len_min_hp 0 -len_max_hp 999 -len_max_indel 999

Thanks,