mapping for dual curation

[evgenyleushkin]

Dear chromap developers,

I'm using chromap for HiC mapping in scaffolding/curation de novo assemblies.
I am very happy with performance, when mapping to one haplotype.
However, we currently practising dual curation, where we map HiC to hap1 and hap2 fastas concatnenated together.
When doing that lots of reads get discarded, and resulting map looks scarce.

Trying different -q (also including 0), doesn't seem to help.
In the log I noticed --max-num-best-mappings parameter (set to 1 by default), trying to change it also didn't change things.

Is it in general possible to map with chromap to a diploid genome version like we do?

Best,

Evgeny

[haowenz]

Chromap is not designed for this specific purpose.
@mourisl Do you think there is a good way to tune parameters of Chromap for this case?