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iqbal-lab-org / gramtools

Genome inference from a population reference graph
MIT License
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Code is too slow - can I have a 50000x speedup please? #76

Closed iqbal-lab closed 6 years ago

ffranr commented 6 years ago

No problemo!

iqbal-lab commented 6 years ago

So you stick to your previous speed timings? Great news

ffranr commented 6 years ago

As far as I can tell, it's performing correctly on WG and Chr10. Had 100% coverage on simulated reads, the allele coverage output file looked reasonable, all tests pass.

iqbal-lab commented 6 years ago

"Previously, generating the kmer index for the wg dataset and kmers of size 15 took a total time of 14461894 seconds split over 3167 cores. After the rewrite, the kmer index for kmer size 15 is generated in 296 seconds on a single core." Closing.

sm0179 commented 6 years ago

Awesome news, thanks Robyn!

Sent from my iPhone

On 30 Oct 2017, at 11:51, Zamin Iqbal notifications@github.com<mailto:notifications@github.com> wrote:

"Previously, generating the kmer index for the wg dataset and kmers of size 15 took a total time of 14461894 seconds split over 3167 cores. After the rewrite, the kmer index for kmer size 15 is generated in 296 seconds on a single core." Closing.

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