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Replace MakeBioSequence call by NewBioSequence call,

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Implements a new file format guesser
Adds some more API doc


Former-commit-id: 9837bf1c28beca6ddb599b367f93548950ba83c1
This commit is contained in:
Eric Coissac
2023-08-30 19:59:46 +02:00
parent c2533667b2
commit 3f8c0d6a2f
7 changed files with 582 additions and 116 deletions
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27
pkg/obialign/alignment.go
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@ -8,21 +8,30 @@ import (
"fmt"
"math"
"strings"
"sync"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
// A pool of byte slices.
var _BuildAlignArenaPool = sync.Pool{
New: func() interface{} {
bs := make([]byte, 0, 300)
return &bs
},
}
// // A pool of byte slices.
// var _BuildAlignArenaPool = sync.Pool{
// New: func() interface{} {
// bs := make([]byte, 0, 300)
// return &bs
// },
// }
// _BuildAlignment builds the alignment between two sequences.
//
// It takes two sequences, a path, a gap character, and two buffers, and it builds the alignment by
// walking the path and copying the sequences into the buffers
// walking the path and copying the sequences into the buffers.
//
// Parameters:
// - seqA: a byte slice representing the first sequence.
// - seqB: a byte slice representing the second sequence.
// - path: a slice of integers representing the alignment path.
// - gap: a byte representing the gap character.
// - bufferA: a pointer to a byte slice for storing the aligned sequence A.
// - bufferB: a pointer to a byte slice for storing the aligned sequence B.
func _BuildAlignment(seqA, seqB []byte, path []int, gap byte, bufferA, bufferB *[]byte) {
*bufferA = (*bufferA)[:0]