some cleaning

pkg/obiiter/fragment.go

@@ -19,7 +19,7 @@ func IFragments(minsize, length, overlap, size, nworkers int) Pipeable {
 			newiter.WaitAndClose()
 		}()
 
-		f := func(iterator IBioSequence, id int) {
+		f := func(iterator IBioSequence) {
 			source := ""
 			for iterator.Next() {
 				news := obiseq.MakeBioSequenceSlice()
@@ -66,9 +66,9 @@ func IFragments(minsize, length, overlap, size, nworkers int) Pipeable {
 		}
 
 		for i := 1; i < nworkers; i++ {
-			go f(iterator.Split(), i)
+			go f(iterator.Split())
 		}
-		go f(iterator, 0)
+		go f(iterator)
 
 		return newiter.SortBatches().Rebatch(size)
 	}

pkg/obioptions/version.go

@@ -8,7 +8,7 @@ import (
 // corresponds to the last commit, and not the one when the file will be
 // commited
 
-var _Commit = "51d11aa"
+var _Commit = "8671285"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.

pkg/obiseq/taxonomy_classifier.go

@@ -31,7 +31,7 @@ func TaxonomyClassifier(taxonomicRank string,
 		if taxon != nil {
 			ttaxon := taxon.TaxonAtRank(taxonomicRank)
 			if abortOnMissing && ttaxon == nil {
-				log.Fatalf("Taxon at rank %s not found in taxonomy for taxid %d", taxonomicRank, taxon.String())
+				log.Fatalf("Taxon at rank %s not found in taxonomy for taxid %s", taxonomicRank, taxon.String())
 			}
 		} else {
 			if abortOnMissing {

pkg/obiseq/taxonomy_predicate.go

@@ -25,7 +25,7 @@ func IsAValidTaxon(taxonomy *obitax.Taxonomy, withAutoCorrection ...bool) Sequen
 				if autocorrection {
 					sequence.SetTaxid(ttaxid)
 					log.Printf(
-						"Sequence %s : Taxid %d updated with %d",
+						"Sequence %s : Taxid %s updated with %s",
 						sequence.Id(),
 						taxid,
 						ttaxid,

pkg/obitools/obiclean/graph.go

@@ -52,35 +52,6 @@ func makeEdge(father, dist, pos int, from, to byte) Edge {
 	}
 }
 
-func abs(x int) int {
-	if x < 0 {
-		return -x
-	}
-	return x
-}
-
-func max(x, y int) int {
-	if x > y {
-		return x
-	}
-	return y
-}
-
-func min(x, y int) int {
-	if x < y {
-		return x
-	}
-	return y
-}
-
-func minMax(x, y int) (int, int) {
-	if x < y {
-		return x, y
-	}
-	return y, x
-
-}
-
 // It takes a filename and a 2D slice of floats pruduced during graph building,
 // and writes a CSV file with the first column being the
 // first nucleotide, the second column being the second nucleotide, and the third column being the

pkg/obitools/obiclean/obiclean.go

@@ -57,9 +57,7 @@ func buildSamples(dataset obiseq.BioSequenceSlice,
 	return samples
 }
 
-func annotateOBIClean(source string, dataset obiseq.BioSequenceSlice,
-	sample map[string]*([]*seqPCR),
-	tag, NAValue string) obiiter.IBioSequence {
+func annotateOBIClean(source string, dataset obiseq.BioSequenceSlice) obiiter.IBioSequence {
 	batchsize := 1000
 	var annot = func(data obiseq.BioSequenceSlice) (obiseq.BioSequenceSlice, error) {
 
@@ -365,7 +363,7 @@ func CLIOBIClean(itertator obiiter.IBioSequence) obiiter.IBioSequence {
 		EmpiricalDistCsv(RatioTableFilename(), all_ratio)
 	}
 
-	iter := annotateOBIClean(source, db, samples, SampleAttribute(), "NA")
+	iter := annotateOBIClean(source, db)
 
 	if OnlyHead() {
 		iter = iter.FilterOn(IsHead, obidefault.BatchSize())