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correction of several small bugs

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This commit is contained in:
Eric Coissac
2024-09-03 06:08:07 -03:00
parent 373464cb06
commit 65ae82622e
22 changed files with 770 additions and 79 deletions
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3
pkg/obingslibrary/marker.go
View File

@ -2,9 +2,10 @@ package obingslibrary
import (
"fmt"
"log"
"strings"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiapat"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"

29
pkg/obingslibrary/multimatch.go
View File

@ -3,7 +3,7 @@ package obingslibrary
import (
"fmt"
"math"
"sort"
"slices"
log "github.com/sirupsen/logrus"
@ -87,6 +87,8 @@ func lookForTag(seq string, delimiter byte) string {
i := len(seq) - 1
// log.Warnf("Provided fragment : %s", string(seq))
for i >= 0 && seq[i] != delimiter {
i--
}
@ -107,6 +109,7 @@ func lookForTag(seq string, delimiter byte) string {
return ""
}
// log.Warnf("extracted : %s", string(seq[begin:end]))
return seq[begin:end]
}
@ -172,11 +175,12 @@ func (marker *Marker) beginDelimitedTagExtractor(
begin int,
forward bool) string {
taglength := marker.Forward_spacer + marker.Forward_tag_length
// log.Warn("beginDelimitedTagExtractor")
taglength := 2*marker.Forward_spacer + marker.Forward_tag_length
delimiter := marker.Forward_tag_delimiter
if !forward {
taglength = marker.Reverse_spacer + marker.Reverse_tag_length
taglength = 2*marker.Reverse_spacer + marker.Reverse_tag_length
delimiter = marker.Reverse_tag_delimiter
}
@ -240,6 +244,7 @@ func (marker *Marker) endDelimitedTagExtractor(
sequence *obiseq.BioSequence,
end int,
forward bool) string {
// log.Warn("endDelimitedTagExtractor")
taglength := marker.Reverse_spacer + marker.Reverse_tag_length
delimiter := marker.Reverse_tag_delimiter
@ -335,14 +340,17 @@ func (marker *Marker) beginTagExtractor(
sequence *obiseq.BioSequence,
begin int,
forward bool) string {
// log.Warnf("Forward : %v -> %d %c", forward, marker.Forward_spacer, marker.Forward_tag_delimiter)
// log.Warnf("Forward : %v -> %d %c", forward, marker.Reverse_spacer, marker.Reverse_tag_delimiter)
if forward {
if marker.Forward_tag_delimiter == 0 {
return marker.beginFixedTagExtractor(sequence, begin, forward)
} else {
if marker.Forward_tag_indels == 0 {
// log.Warnf("Delimited tag for forward primers %s", marker.forward.String())
return marker.beginDelimitedTagExtractor(sequence, begin, forward)
} else {
// log.Warn("Rescue tag for forward primers")
// log.Warnf("Rescue tag for forward primers %s", marker.forward.String())
return marker.beginRescueTagExtractor(sequence, begin, forward)
}
}
@ -351,9 +359,10 @@ func (marker *Marker) beginTagExtractor(
return marker.beginFixedTagExtractor(sequence, begin, forward)
} else {
if marker.Reverse_tag_indels == 0 {
// log.Warnf("Delimited tag for reverse/complement primers %s", marker.creverse.String())
return marker.beginDelimitedTagExtractor(sequence, begin, forward)
} else {
// log.Warn("Rescue tag for reverse/complement primers")
// log.Warnf("Rescue tag for reverse/complement primers %s", marker.creverse.String())
return marker.beginRescueTagExtractor(sequence, begin, forward)
}
}
@ -369,9 +378,10 @@ func (marker *Marker) endTagExtractor(
return marker.endFixedTagExtractor(sequence, end, forward)
} else {
if marker.Reverse_tag_indels == 0 {
// log.Warnf("Delimited tag for reverse primers %s", marker.reverse.String())
return marker.endDelimitedTagExtractor(sequence, end, forward)
} else {
// log.Warn("Rescue tag for reverse primers")
// log.Warnf("Rescue tag for reverse primers %s", marker.reverse.String())
return marker.endRescueTagExtractor(sequence, end, forward)
}
}
@ -380,9 +390,10 @@ func (marker *Marker) endTagExtractor(
return marker.endFixedTagExtractor(sequence, end, forward)
} else {
if marker.Forward_tag_indels == 0 {
// log.Warnf("Delimited tag for forward/complement primers %s", marker.cforward.String())
return marker.endDelimitedTagExtractor(sequence, end, forward)
} else {
// log.Warn("Rescue tag for forward/complement primers")
// log.Warnf("Rescue tag for forward/complement primers %s", marker.cforward.String())
return marker.endRescueTagExtractor(sequence, end, forward)
}
}
@ -609,9 +620,7 @@ func (library *NGSLibrary) ExtractMultiBarcode(sequence *obiseq.BioSequence) (ob
}
if len(matches) > 0 {
sort.Slice(matches, func(i, j int) bool {
return matches[i].Begin < matches[j].Begin
})
slices.SortFunc(matches, func(a, b PrimerMatch) int { return a.Begin - b.Begin })
state := 0
var from PrimerMatch

5
pkg/obingslibrary/ngslibrary.go
View File

@ -36,8 +36,9 @@ func MakeNGSLibrary() NGSLibrary {
}
func (library *NGSLibrary) GetMarker(forward, reverse string) (*Marker, bool) {
pair := PrimerPair{strings.ToLower(forward),
strings.ToLower(reverse)}
forward = strings.ToLower(forward)
reverse = strings.ToLower(reverse)
pair := PrimerPair{forward, reverse}
marker, ok := (library.Markers)[pair]
if ok {