Bit-packing single nucleotide bases

Checking-ACGT	Bitwise-operation	Method	Time(ns)
	yes	base2int_nochecking	20.55
yes		base2int_array	24.96
yes	yes	base2int_bitwise	30.77
yes	yes	base2int_if	49.99
yes		base2int_switch	51.43
yes	yes	base2int_bytes_index	130.8

Notes:

1. K-mer encoding: A=0, C=1, T=2, G=3
2. The base2int functions check bases, while the benchmark codes skip it.
3. go version go1.19rc2 linux/amd64

Run the bencmark

# test
$ go test

# bench
$ go test -bench Bench*

Links

Packages:

• (Go) kmers - Bit-packed k-mers methods for Golang
• (Rust) nuc2bit - A rust crate that provides methods for rapidly encoding and decoding nucleotides in 2-bit representation.
• (C) kmer-cnt - Code examples of fast and simple k-mer counters for tutorial purposes
• ...

Tutorials:

• how to encode char in 2-bits?