Chaim Schramm

Here's another vote for docopt handling this natively

Yes, this is a known issue. The main cause is large 10x datasets with droplets containing 10s of (usually light) chains that trigger an inordinate [number of alignments trying to...

I sent you a link to a tarball in google drive

It helped with the kappas, but not the heavy chain (for this one test cell): ``` $ head test-Hpseud/filtered_BCR_seqs/filtered_BCRs.txt ------------------ test2 ------------------ BCR_H recombinants: 0/0 BCR_K recombinants: 0/2 BCR_L recombinants:...

Related: `--V_gapped` is also documented as optional, but `bracer assemble` doesn't test for the absence of the gapped files and so this also causes a crash.

I ran `bracer build` for all 3 loci before attempting `bracer assemble`.