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Add the possibility to look for patterns allowing indels.

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Former-commit-id: 0599c2b0ad16df086dbdb08e491503870d8904be
This commit is contained in:
Eric Coissac
2023-03-20 15:28:24 +07:00
parent 5fbe52368c
commit 27d6c60e25
14 changed files with 674 additions and 219 deletions
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8
pkg/obiapat/pcr.go
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@ -133,7 +133,7 @@ func OptionForwardPrimer(primer string, max int) WithOption {
f := WithOption(func(opt Options) {
var err error
opt.pointer.forward, err = MakeApatPattern(primer, max)
opt.pointer.forward, err = MakeApatPattern(primer, max, false)
if err != nil {
log.Fatalf("error : %v\n", err)
}
@ -155,7 +155,7 @@ func OptionReversePrimer(primer string, max int) WithOption {
f := WithOption(func(opt Options) {
var err error
opt.pointer.reverse, err = MakeApatPattern(primer, max)
opt.pointer.reverse, err = MakeApatPattern(primer, max, false)
if err != nil {
log.Fatalf("error : %v\n", err)
}
@ -210,7 +210,7 @@ func _Pcr(seq ApatSequence,
reverse := opt.pointer.reverse
crev := opt.pointer.crev
forwardMatches := forward.FindAllIndex(seq)
forwardMatches := forward.FindAllIndex(seq,0,-1)
if len(forwardMatches) > 0 {
@ -284,7 +284,7 @@ func _Pcr(seq ApatSequence,
}
}
forwardMatches = reverse.FindAllIndex(seq)
forwardMatches = reverse.FindAllIndex(seq,0,-1)
if forwardMatches != nil {
begin := forwardMatches[0][0]