update the geometric obitag

Former-commit-id: acd8fe1c8c1cf443098432d818397b0b5d02df33

.gitignore

@@ -116,3 +116,4 @@ doc/book/wolf_data/Release-253/ncbitaxo/names.dmp
 doc/book/wolf_data/Release-253/ncbitaxo/nodes.dmp
 doc/book/wolf_data/Release-253/ncbitaxo/readme.txt
 doc/book/results/toto.tasta
+sample/.DS_Store

pkg/obistats/kmeans.go

@@ -15,14 +15,14 @@ import (
 // SquareDist calculates the squared Euclidean distance between
 // two vectors 'a' and 'b'.
 //
-// 'a' and 'b' are slices of float64 values representing
+// 'a' and 'b' are slices of float64 or int values representing
 // coordinate points in space. It is assumed that both slices
 // have the same length.
 // Returns the calculated squared distance as a float64.
-func SquareDist[T float64 | int](a, b []T) float64 {
-	sum := 0.0
+func SquareDist[T float64 | int](a, b []T) T {
+	sum := T(0)
 	for i, v := range a {
-		diff := float64(v - b[i])
+		diff := v - b[i]
 		sum += diff * diff
 	}
 	return sum
@@ -35,7 +35,7 @@ func SquareDist[T float64 | int](a, b []T) float64 {
 // is paired with the corresponding element of `b`.
 // Returns the squared sum of the differences.
 func EuclideanDist[T float64 | int](a, b []T) float64 {
-	return math.Sqrt(SquareDist(a, b))
+	return math.Sqrt(float64(SquareDist(a, b)))
 }
 
 // DefaultRG creates and returns a new instance of *rand.Rand.

pkg/obitools/obirefidx/geomindexing.go

@@ -6,6 +6,7 @@ import (
 	"sort"
 	"sync"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obistats"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
@@ -24,26 +25,36 @@ func GeomIndexSesquence(seqidx int,
 		log.Fatalf("Sequence %s does not have a coordinate", sequence.Id())
 	}
 
-	seq_dist := make([]float64, len(references))
+	seq_dist := make([]int, len(references))
 
 	var wg sync.WaitGroup
 
-	for i, ref := range references {
-		wg.Add(1)
-		go func(i int, ref *obiseq.BioSequence) {
-			defer wg.Done()
-			reflocation := ref.GetCoordinate()
-			if reflocation == nil {
-				log.Fatalf("Sequence %s does not have a coordinate", ref.Id())
-			}
+	iseq_channel := make(chan int)
 
-			seq_dist[i] = obistats.SquareDist(location, reflocation)
-		}(i, ref)
+	for k := 0; k < obioptions.CLIParallelWorkers(); k++ {
+		wg.Add(1)
+		go func() {
+			defer wg.Done()
+			for i := range iseq_channel {
+				ref := references[i]
+				reflocation := ref.GetCoordinate()
+				if reflocation == nil {
+					log.Fatalf("Sequence %s does not have a coordinate", ref.Id())
+				}
+
+				seq_dist[i] = obistats.SquareDist(location, reflocation)
+			}
+		}()
 	}
 
+	for i := range references {
+		iseq_channel <- i
+	}
+
+	close(iseq_channel)
 	wg.Wait()
 
-	order := obiutils.Order(sort.Float64Slice(seq_dist))
+	order := obiutils.Order(sort.IntSlice(seq_dist))
 
 	lca := (*taxa)[seqidx]
 

pkg/obitools/obitag/obigeomtag.go

@@ -1,7 +1,7 @@
 package obitag
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 	"math"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
@@ -99,9 +99,9 @@ func MapOnLandmarkSequences(sequence *obiseq.BioSequence, landmarks *obiseq.BioS
 func FindGeomClosest(sequence *obiseq.BioSequence,
 	landmarks *obiseq.BioSequenceSlice,
 	references *obiseq.BioSequenceSlice,
-	buffer *[]uint64) (*obiseq.BioSequence, float64, float64, []int, *obiseq.BioSequenceSlice) {
+	buffer *[]uint64) (*obiseq.BioSequence, int, float64, []int, *obiseq.BioSequenceSlice) {
 
-	min_dist := math.MaxFloat64
+	min_dist := math.MaxInt
 	min_idx := make([]int, 0)
 
 	query_location := MapOnLandmarkSequences(sequence, landmarks, buffer)
@@ -129,7 +129,7 @@ func FindGeomClosest(sequence *obiseq.BioSequence,
 
 	for _, i := range min_idx {
 		seq := (*references)[i]
-		lcs, length := obialign.FastLCSEGFScore(sequence, seq, -1, buffer)
+		lcs, length := obialign.FastLCSScore(sequence, seq, -1, buffer)
 		ident := float64(lcs) / float64(length)
 		if ident > best_id {
 			best_id = ident

pkg/obitools/obitag/obitag.go

@@ -29,20 +29,19 @@ import (
 // - taxid: The taxid associated with the matched distance.
 // - rank: The rank associated with the matched distance.
 // - scientificName: The scientific name associated with the matched distance.
-func MatchDistanceIndex(distance float64, distanceIdx map[int]string) (int, string, string) {
-	idist := int(distance)
+func MatchDistanceIndex(distance int, distanceIdx map[int]string) (int, string, string) {
 	keys := maps.Keys(distanceIdx)
 	slices.Sort(keys)
 
 	i := sort.Search(len(keys), func(i int) bool {
-		return idist <= keys[i]
+		return distance <= keys[i]
 	})
 
 	var taxid int
 	var rank string
 	var scientificName string
 
-	if i == len(keys) || idist > keys[len(keys)-1] {
+	if i == len(keys) || distance > keys[len(keys)-1] {
 		taxid = 1
 		rank = "no rank"
 		scientificName = "root"