Daniel Standage

Got it. So at some point we need to print out the random seed being used so that when tests fail we can reproduce their behavior, right?

> If we do everything right in writing the tests they always use the same seed on all the platforms. Ah, I see. I misunderstood. In contrast, the GenomeTools library...

I think @wltrimbl is right here. I'm starting to connect some dots here. I spent an inordinate amount of time last night troubleshooting a Docker build issue for kevlar. I...

> Am I understanding correctly that for Nodegraph, the n_tables is the same as the number of hash functions, i.e. k in the wikpedia? And is the tablesize the same...

I don't know if khmer provides any way to do this out-of-the-box. The problem is that the CountMin sketch (`Countgraph` or `Counttable` objects in khmer) don't store the k-mer sequence,...

Hi @IzhLab! If you’re only going to be storing the reads in a counttable or countgraph, then pairing info is not required. You can simply consume one file and then...

Ok, I made some changes to `storage.hh` and it now behaves as expected: quicker runtime, all queries return 0. ``` $ # Branch "master" $ python eval.py full.fq ...iteration 1...

This depends on `consume_seqfile_banding_with_reads_parser` from #1753.

Some initial benchmarking this weekend: ran `abund-dist-single.py` with & without banding (`--banding 8 1`) and with & without threading (`--threads 4`). Banding *does* provide a runtime performance improvement, but it...

Hmm. The cyclic hash is not only faster than the murmur hash (we already knew that), but its speed benefits seem to stack better with threading. The commands I used:...