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Add option related to agrep match on obigrep and obiannotate

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This commit is contained in:
Eric Coissac
2024-09-09 16:52:13 +02:00
parent 65ae82622e
commit 05bf2bfd6c
12 changed files with 167 additions and 34 deletions
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11
pkg/obialign/locatepattern.go
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@ -25,17 +25,18 @@ func buffIndex(i, j, width int) int {
//
// The function returns the start and end positions of the best
// match, as well as the number of errors in the best match.
func LocatePattern(pattern, sequence []byte) (int, int, int) {
func LocatePattern(id string, pattern, sequence []byte) (int, int, int) {
if len(pattern) >= len(sequence) {
log.Panicf("Sequence %s:Pattern %s must be shorter than sequence %s", id, pattern, sequence)
}
// Pattern spreads over the columns
// Sequence spreads over the rows
width := len(pattern) + 1
buffsize := (len(pattern) + 1) * (len(sequence) + 1)
buffer := make([]int, buffsize)
if len(pattern) >= len(sequence) {
log.Panicf("Pattern %s must be shorter than sequence %s", pattern, sequence)
}
// The path matrix keeps track of the best path through the matrix
// 0 : indicate the diagonal path
// 1 : indicate the up path