K-mer counting with threads#107
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Will need to wait to merge this until dib-lab/khmer#1753 is merged. |
Codecov Report
@@ Coverage Diff @@
## master #107 +/- ##
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+ Coverage 89.62% 90.57% +0.95%
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Files 32 32
Lines 1552 1560 +8
Branches 247 249 +2
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+ Hits 1391 1413 +22
+ Misses 112 98 -14
Partials 49 49
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In #102 I started exploring parallel k-mer counting. With the 1-thread-per-sample approach, the most I can hope for is a 3-4x speedup for processing a simplex. Looking more closely at some of the khmer scripts, I figured it would be much better to process one sample at a time but using as many threads as the user can spare. This indeed seems to be giving great speedups. Will post numbers soon.
Runtime for
kevlar countandkevlar novelis one of the big pain points right now, and this PR should bring the days of required processing time down to hours.