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Code refactoring

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This commit is contained in:
Eric Coissac
2022-01-14 15:36:39 +01:00
parent 402d54cb62
commit 2163db94d0
4 changed files with 32 additions and 24 deletions
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14
pkg/obialign/fourbitsencode.go
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@ -4,7 +4,7 @@ import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
var __four_bits_base_code__ = []byte{0b0000,
var _FourBitsBaseCode = []byte{0b0000,
// IUPAC nucleotide code Base
0b0001, // A Adenine
0b1110, // B C or G or T
@ -38,7 +38,7 @@ var __four_bits_base_code__ = []byte{0b0000,
0b0000,
0b0000}
var __four_bits_base_decode__ = []byte{
var _FourBitsBaseDecode = []byte{
// 0b0000 0b0001 0b0010 0b0011
'.', 'a', 'c', 'm',
// 0b0100 0b0101 0b0110 0b0111
@ -49,6 +49,14 @@ var __four_bits_base_decode__ = []byte{
'k', 'd', 'b', 'n',
}
// Encode4bits encodes each nucleotide of a sequence into a binary
// code where the four low weigth bit of a byte correspond respectively
// to the four nucleotides A, C, G, T. Simple bases A, C, G, T are therefore
// represented by a code with only a single bit on, when anbiguous symboles
// like R, D or N have the bits corresponding to each nucleotide represented
// by the ambiguity set to 1.
// A byte slice can be provided (buffer) to preveent allocation of a new
// memory chunk by th function.
func Encode4bits(seq obiseq.BioSequence, buffer []byte) []byte {
length := seq.Length()
rawseq := seq.Sequence()
@ -65,7 +73,7 @@ func Encode4bits(seq obiseq.BioSequence, buffer []byte) []byte {
if nuc == '.' || nuc == '-' {
code = 0
} else {
code = __four_bits_base_code__[nuc&31]
code = _FourBitsBaseCode[nuc&31]
}
buffer = append(buffer, code)
}