This package provides manipulations for bit-packed k-mers (k<=32, encoded in uint64).
Methods with names starting with Must are faster by skipping boundary checking.
Related projects:
- unik provides k-mer serialization methods for this package.
- unikmer, a toolkit for nucleic acid k-mer analysis, including set operations on k-mers optional with TaxIDs.
- sketches provides generators/iterators for k-mer sketches (Minimizer, Scaled MinHash, Closed Syncmers).
CPU: AMD Ryzen 7 2700X Eight-Core Processor, 3.7 GHz
$ go test . -bench=Bench* -benchmem \
| grep Bench \
| perl -pe 's/\s\s+/\t/g' \
| csvtk cut -Ht -f 1,3-5 \
| csvtk add-header -t -n test,time,memory,allocs \
| csvtk pretty -t -r
test time memory allocs
------------------------------------------ ------------ -------- -----------
BenchmarkEncodeK32-16 19.67 ns/op 0 B/op 0 allocs/op
BenchmarkEncodeFromFormerKmerK32-16 7.692 ns/op 0 B/op 0 allocs/op
BenchmarkMustEncodeFromFormerKmerK32-16 2.008 ns/op 0 B/op 0 allocs/op
BenchmarkDecodeK32-16 80.73 ns/op 32 B/op 1 allocs/op
BenchmarkMustDecodeK32-16 76.93 ns/op 32 B/op 1 allocs/op
BenchmarkRevK32-16 3.617 ns/op 0 B/op 0 allocs/op
BenchmarkCompK32-16 0.7999 ns/op 0 B/op 0 allocs/op
BenchmarkRevCompK32-16 3.814 ns/op 0 B/op 0 allocs/op
BenchmarkCannonalK32-16 4.147 ns/op 0 B/op 0 allocs/op
Please open an issue to report bugs, propose new functions or ask for help.
This package was originally maintained in unikmer.