Merging and then unmerging small contigs

Question

[Philipp Bayer]

We've been using mosdepth a lot for coverage calculation of plant pangenomes but it starts to choke when you have many, many tiny contigs instead of a few large chromosomes because of the way the algorithm works.

I'm wondering - is there any tool which can take bam files of reads aligned to those contigs, then make a fake 'pseudomolecule' out of the contigs keeping in mind where each contig is located, then uses that to make a new bam file with the reads moved over to that fake pseudomolecule? That way I could run mosdepth much faster and then later change the resulting per-base coverage bed file back into the original contigs.

I'd write it myself but there are several chances to introduce off-by-one errors and I know I'll hit them all.