Brice Letcher

How about https://github.com/edawson/gfakluge ? Though i don't think it supports rGFA.

Hi @khodor14 , what is the FILTER status of the calls in your VCF? `gramtools` will only put variants with FILTER set to PASS in the constructed graph.

Targets here: 1. We want to be able to build a PRG from a MSA right now 1. Long alleles might need to be collapsed down. For eg a record...

Now that gramtools supports prgs made with [make_prg](https://github.com/iqbal-lab-org/make_prg), we need a streamlined way to build a whole-genome graph from: * a ref genome * a set of MSAs (as a...

Hi @kdm9 , this is a timely question! The feature is not currently implemented in a simple way at all, I've done it via a snakemake worfklow. I will aim...

commit | command | dataset | kmer size | peak RAM (GBytes | average RAM (Gbytes) | run time (seconds) | CPU time (seconds) | mapped reads per CPU sec...

@leoisl has noticed one (probably) bug and one possible improvement: 1. [Bug] At https://github.com/iqbal-lab-org/gramtools/blob/master/libgramtools/src/quasimap/coverage/grouped_allele_counts.cpp#L52 : when an allele combination has not been seen before, an entry is created in the...

In response to this: > @leoisl has noticed one (probably) bug and one possible improvement: > > 1. [Bug] At https://github.com/iqbal-lab-org/gramtools/blob/master/libgramtools/src/quasimap/coverage/grouped_allele_counts.cpp#L52 : > when an allele combination has not been...

Here is what happens under https://github.com/bricoletc/gramtools/commit/e66865ebdf6a14b56ac4ed4e6759a6509ddc9835 ; the instruction #pragma omp atomic is changed to #pragma omp critical in libgramtools/src/quasimap/coverage/grouped_allele_counts.cpp, now threads cannot update grouped coverage simulateneously.  Some samples...

#149 reduced index size by roughly a factor of the average number of alleles per site