Hifiasm: create alt contigs

[MartinPippel]

Is your feature request related to a problem? Please describe.
In the current pipeline we are not using HiC phasing option. But we probably should produce the alt contigs (a_ctg) by providing the --primary flag in the meantime and integrate these into pipeline (merqury plots, merging purged p_ctg and a_ctg and rerun purging, etc).

The documentation of all possible output files of hifiasm is provided here: hifiasm_interpreting-output