`--rl-cut` also filters CCS HiFi reads in `hybrid_v1` with `--ont --hf`

[hrluo93]

Hi, thank you for developing this excellent program!

In the hybrid_v1 branch, --rl-cut is documented as filtering short ONT Simplex reads. However, when --ont and --hf are used together, the same threshold also appears to be applied to the CCS/HiFi input.

I found that setting a high ONT cutoff, for example --rl-cut 59999, removes all normal-length CCS reads from the hybrid correction dataset.
hifiasm --ont --rl-cut 59999 --hf 145ji.hifi_reads.fq.gz --hyb-syn 3 --telo-m CCCTAA -t 32 -o eeu60khybrid *.sup.5mc.fq.gz
"[M::yak_count] collected 0 minimizers
-0-[M::cal_ec_r] # tqn::880959, Ont base::75032244859, # HiFi bases::0
[M::ff_ihyb_syn_tid::cis-paf] # syn overlaps::0, # syn informative overlaps::0
[M::ff_ihyb_syn_tid::trans-paf] # syn overlaps::0, # syn informative overlaps::0
[M::pec::4293.247] # bases: 75032244859; # corrected bases: 511408722"

Then, I performed:

seqkit seq -m 59999 *.sup.5mc.fq.gz -o sample.ont.ge60k.fq.gz

hifiasm --ont --hf 145ji.hifi_reads.fq.gz --hyb-syn 3 --telo-m CCCTAA -t 32 -o eeu60khybrid sample.ont.ge60k.fq.gz
"-0-[M::cal_ec_r] # tqn::880959, Ont base::75032244859, # HiFi bases::43785201274
[M::ff_ihyb_syn_tid::cis-paf] # syn overlaps::108738511, # syn informative overlaps::102157482
[M::ff_ihyb_syn_tid::trans-paf] # syn overlaps::64663404, # syn informative overlaps::0
"

Best wishes!
Haoran