JoshuaDanielRubin
JoshuaDanielRubin
Ah, I see. Thanks!
I do not know how to add myself to Assignees but I plan to work on this.
Another idea for mtDNA haplotype calling could be the HaploCart subcommand of vgan: https://github.com/grenaud/vgan HaploCart uses a pangenome graph (based on the VG model) and is not biased towards any...
This pull request is in place of #635. The added test input file are simulated single-end reads from the rCRS reference genome.
@jfy133 Requesting review
Ok thank you both for the help and suggestions! I will keep working on this.
Hi @jfy133, sorry for the delay here, to be honest I got stuck with the tests failing. And I am a bit behind with PhD work unfortunately at cannot really...
Hi @aidaanva, (Sorry for the late reply, I was on vacation.) Thank you for working on this! I really appreciate the help. It looks like the reads are not being...
@aidaanva Yes, the rCRS is mitochondrial. So this is strange that not a single read is mapping. May I ask what the contents of the stacktrace are in the file...
Also, just to be sure, the --hcfiles argument is pointing to the directory with the haplocart files?