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optimize sequence readers and patch a bug in the format guesser

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Former-commit-id: 9dce1e96c57ae9a88c26fac5c8e1bdcdc2c0c7a5
This commit is contained in:
Eric Coissac
2023-10-13 21:52:57 +02:00
parent ddf0f2cede
commit e8c55a2b6b
7 changed files with 141 additions and 46 deletions
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124
pkg/obiapat/pcr.go
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@ -14,6 +14,7 @@ type _Options struct {
forwardError int
reverseError int
extension int
fullExtension bool
batchSize int
parallelWorkers int
forward ApatPattern
@ -41,6 +42,10 @@ func (options Options) Extension() int {
return options.pointer.extension
}
func (options Options) OnlyFullExtension() bool {
return options.pointer.fullExtension
}
// MinLength method returns minimum length of
// the searched amplicon (length of the primers
// excluded)
@ -96,6 +101,7 @@ func MakeOptions(setters []WithOption) Options {
forwardError: 0,
reverseError: 0,
extension: -1,
fullExtension: false,
circular: false,
parallelWorkers: 4,
batchSize: 100,
@ -172,6 +178,14 @@ func OptionWithExtension(extension int) WithOption {
return f
}
func OptionOnlyFullExtension(full bool) WithOption {
f := WithOption(func(opt Options) {
opt.pointer.fullExtension = full
})
return f
}
// OptionForwardError sets the number of
// error allowed when matching the forward
// primer.
@ -285,31 +299,51 @@ func _Pcr(seq ApatSequence,
from = fm[1]
to = rm[0]
}
amplicon, _ := seq.pointer.reference.Subsequence(from, to, opt.pointer.circular)
log.Debugf("seq length : %d capacity : %d", amplicon.Len(), cap(amplicon.Sequence()))
annot := amplicon.Annotations()
obiutils.MustFillMap(annot, seq.pointer.reference.Annotations())
annot["forward_primer"] = forward.String()
if opt.HasExtension() && !opt.OnlyFullExtension() && !opt.Circular() {
if from < 0 {
from = 0
}
if to > seq.Len() {
to = seq.Len()
}
}
match, _ := seq.pointer.reference.Subsequence(fm[0], fm[1], opt.pointer.circular)
annot["forward_match"] = match.String()
match.Recycle()
if (opt.HasExtension() && ((from >= 0 && to <= seq.Len()) || opt.Circular())) ||
!opt.HasExtension() {
annot["forward_error"] = erri
amplicon, error := seq.pointer.reference.Subsequence(from, to, opt.Circular())
annot["reverse_primer"] = reverse.String()
match, _ = seq.pointer.reference.Subsequence(rm[0], rm[1], opt.pointer.circular)
match = match.ReverseComplement(true)
annot["reverse_match"] = match.String()
match.Recycle()
if error != nil {
log.Fatalf("error : %v\n", error)
}
annot["reverse_error"] = errj
annot["direction"] = "forward"
log.Debugf("seq length : %d capacity : %d", amplicon.Len(), cap(amplicon.Sequence()))
annot := amplicon.Annotations()
obiutils.MustFillMap(annot, seq.pointer.reference.Annotations())
// log.Debugf("amplicon sequence capacity : %d", cap(amplicon.Sequence()))
annot["forward_primer"] = forward.String()
results = append(results, amplicon)
match, _ := seq.pointer.reference.Subsequence(fm[0], fm[1], opt.pointer.circular)
annot["forward_match"] = match.String()
match.Recycle()
annot["forward_error"] = erri
annot["reverse_primer"] = reverse.String()
match, _ = seq.pointer.reference.Subsequence(rm[0], rm[1], opt.pointer.circular)
match = match.ReverseComplement(true)
annot["reverse_match"] = match.String()
match.Recycle()
annot["reverse_error"] = errj
annot["direction"] = "forward"
// log.Debugf("amplicon sequence capacity : %d", cap(amplicon.Sequence()))
results = append(results, amplicon)
}
}
}
}
@ -370,30 +404,48 @@ func _Pcr(seq ApatSequence,
from = fm[1]
to = rm[0]
}
amplicon, _ := seq.pointer.reference.Subsequence(from, to, opt.pointer.circular)
amplicon = amplicon.ReverseComplement(true)
annot := amplicon.Annotations()
obiutils.MustFillMap(annot, seq.pointer.reference.Annotations())
annot["forward_primer"] = forward.String()
if opt.HasExtension() && !opt.OnlyFullExtension() && !opt.Circular() {
if from < 0 {
from = 0
}
if to > seq.Len() {
to = seq.Len()
}
}
match, _ := seq.pointer.reference.Subsequence(rm[0], rm[1], opt.pointer.circular)
match.ReverseComplement(true)
annot["forward_match"] = match.String()
match.Recycle()
if (opt.HasExtension() && ((from >= 0 && to <= seq.Len()) || opt.Circular())) ||
!opt.HasExtension() {
amplicon, error := seq.pointer.reference.Subsequence(from, to, opt.pointer.circular)
annot["forward_error"] = errj
if error != nil {
log.Fatalf("error : %v\n", error)
}
annot["reverse_primer"] = reverse.String()
match, _ = seq.pointer.reference.Subsequence(fm[0], fm[1], opt.pointer.circular)
annot["reverse_match"] = match.String()
match.Recycle()
amplicon = amplicon.ReverseComplement(true)
annot["reverse_error"] = erri
annot["direction"] = "reverse"
annot := amplicon.Annotations()
obiutils.MustFillMap(annot, seq.pointer.reference.Annotations())
annot["forward_primer"] = forward.String()
results = append(results, amplicon)
// log.Debugf("amplicon sequence capacity : %d", cap(amplicon.Sequence()))
match, _ := seq.pointer.reference.Subsequence(rm[0], rm[1], opt.pointer.circular)
match.ReverseComplement(true)
annot["forward_match"] = match.String()
match.Recycle()
annot["forward_error"] = errj
annot["reverse_primer"] = reverse.String()
match, _ = seq.pointer.reference.Subsequence(fm[0], fm[1], opt.pointer.circular)
annot["reverse_match"] = match.String()
match.Recycle()
annot["reverse_error"] = erri
annot["direction"] = "reverse"
results = append(results, amplicon)
// log.Debugf("amplicon sequence capacity : %d", cap(amplicon.Sequence()))
}
}
}
}