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Rename the Length methods Len to follow GO standart

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This commit is contained in:
Eric Coissac
2022-11-17 11:09:58 +01:00
parent eb32089305
commit 29563aa94e
30 changed files with 134 additions and 130 deletions
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24
pkg/obiapat/pcr.go
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@ -234,15 +234,15 @@ func _Pcr(seq ApatSequence,
if len(forwardMatches) > 0 {
begin := forwardMatches[0][0]
length := seq.Length() - begin
length := seq.Len() - begin
if opt.pointer.maxLength > 0 {
length = forwardMatches[len(forwardMatches)-1][2] - begin + opt.MaxLength() + reverse.Length()
length = forwardMatches[len(forwardMatches)-1][2] - begin + opt.MaxLength() + reverse.Len()
}
if opt.Circular() {
begin = 0
length = seq.Length() + _MaxPatLen
length = seq.Len() + _MaxPatLen
}
reverseMatches := crev.FindAllIndex(seq, begin, length)
@ -252,13 +252,13 @@ func _Pcr(seq ApatSequence,
posi := fm[0]
if posi < seq.Length() {
if posi < seq.Len() {
erri := fm[2]
for _, rm := range reverseMatches {
posj := rm[0]
if posj < seq.Length() {
if posj < seq.Len() {
posj := rm[1]
errj := rm[2]
length = 0
@ -267,7 +267,7 @@ func _Pcr(seq ApatSequence,
length = rm[0] - fm[1]
} else {
if opt.Circular() {
length = rm[0] + seq.Length() - posi - forward.Length()
length = rm[0] + seq.Len() - posi - forward.Len()
}
}
if length > 0 && // For when primers touch or overlap
@ -307,15 +307,15 @@ func _Pcr(seq ApatSequence,
if forwardMatches != nil {
begin := forwardMatches[0][0]
length := seq.Length() - begin
length := seq.Len() - begin
if opt.pointer.maxLength > 0 {
length = forwardMatches[len(forwardMatches)-1][2] - begin + opt.MaxLength() + reverse.Length()
length = forwardMatches[len(forwardMatches)-1][2] - begin + opt.MaxLength() + reverse.Len()
}
if opt.Circular() {
begin = 0
length = seq.Length() + _MaxPatLen
length = seq.Len() + _MaxPatLen
}
reverseMatches := cfwd.FindAllIndex(seq, begin, length)
@ -325,13 +325,13 @@ func _Pcr(seq ApatSequence,
posi := fm[0]
if posi < seq.Length() {
if posi < seq.Len() {
erri := fm[2]
for _, rm := range reverseMatches {
posj := rm[0]
if posj < seq.Length() {
if posj < seq.Len() {
posj := rm[1]
errj := rm[2]
length = 0
@ -340,7 +340,7 @@ func _Pcr(seq ApatSequence,
length = rm[0] - fm[1]
} else {
if opt.Circular() {
length = rm[0] + seq.Length() - posi - forward.Length()
length = rm[0] + seq.Len() - posi - forward.Len()
}
}
if length > 0 && // For when primers touch or overlap