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rename the iterator class

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This commit is contained in:
Eric Coissac
2023-01-22 22:04:17 +01:00
parent 4592855095
commit f97f92df72
37 changed files with 399 additions and 354 deletions
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11
pkg/obitools/obiclean/obiclean.go
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@@ -19,7 +19,7 @@ type seqPCR struct {
SonCount int
AddedSons int
Edges []Edge
Cluster map[int]bool // used as the set of head sequences associated to that sequence
Cluster map[int]bool // used as the set of head sequences associated to that sequence
}
// buildSamples sorts the sequences by samples
@@ -58,7 +58,7 @@ func buildSamples(dataset obiseq.BioSequenceSlice,
func annotateOBIClean(dataset obiseq.BioSequenceSlice,
sample map[string]*([]*seqPCR),
tag, NAValue string) obiiter.IBioSequenceBatch {
tag, NAValue string) obiiter.IBioSequence {
batchsize := 1000
var annot = func(data obiseq.BioSequenceSlice) obiseq.BioSequenceSlice {
@@ -207,7 +207,6 @@ func GetCluster(sequence *obiseq.BioSequence) map[string]string {
return cluster
}
// func Cluster(sample map[string]*([]*seqPCR)) {
// for _, graph := range sample {
// for _, s := range *graph {
@@ -215,7 +214,7 @@ func GetCluster(sequence *obiseq.BioSequence) map[string]string {
// if len(s.Edges) > 0 {
// for _, f := range s.Edges {
// }
// }
// } else {
// cluster
// }
@@ -286,7 +285,7 @@ func Weight(sequence *obiseq.BioSequence) map[string]int {
return weight
}
func IOBIClean(itertator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
func IOBIClean(itertator obiiter.IBioSequence) obiiter.IBioSequence {
db := itertator.Load()
@@ -318,7 +317,6 @@ func IOBIClean(itertator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
}
}
Mutation(samples)
pbopt := make([]progressbar.Option, 0, 5)
@@ -352,7 +350,6 @@ func IOBIClean(itertator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
EmpiricalDistCsv(RatioTableFilename(), all_ratio)
}
iter := annotateOBIClean(db, samples, SampleAttribute(), "NA")
if OnlyHead() {