rename goutils to obiutils

Former-commit-id: 2147f53db972bba571dfdae30c51b62d3e69cec5

doc/man/test.md

@@ -0,0 +1,20 @@
+% obigrep(1)
+% Eric Coissac
+% February 2023
+# NAME
+
+obigrep -- filters sequence files according to numerous conditions
+
+# SYNOPSIS
+
+**snowplough**␣\[**-h**\]␣\[**--configfile**␣*CONFIGFILE*\]␣\[**--sort**\]␣\[**--vim**\]␣*keyword*␣\[*keyword␣...*\]␣\[**--configfile**␣*CONFIGFILE*\]␣\[**--sort**\]␣\[**--vim**\]␣*keyword*␣\[*keyword␣...*\]␣\[**--configfile**␣*CONFIGFILE*\]␣\[**--sort**\]␣\[**--vim**\]␣*keyword*␣\[*keyword␣...*\]
+
+# DESCRIPTION
+
+**snowplough** is a simple-minded tool which creates indices and body-searches vast quantities of ServiceNow tickets, which is useful to find out how someone before you solved one particular problem.
+
+# GENERAL OPTIONS
+
+**-h**, **--help**
+
+:   Display a friendly help message.

pkg/goutils/minmax.go

@@ -1,37 +0,0 @@
-package goutils
-
-func MinInt(x, y int) int {
-	if x < y {
-		return x
-	}
-	return y
-}
-
-func MaxInt(x, y int) int {
-	if x < y {
-		return y
-	}
-	return x
-}
-
-func MinMaxInt(x, y int) (int,int) {
-	if x < y {
-		return x,y
-	}
-	return y,x
-}
-
-
-func MinUInt16(x, y uint16) uint16 {
-	if x < y {
-		return x
-	}
-	return y
-}
-
-func MaxUInt16(x, y uint16) uint16 {
-	if x < y {
-		return y
-	}
-	return x
-}

pkg/obialign/fastlcs.go

@@ -1,7 +1,7 @@
 package obialign
 
 // import (
-// 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
+// 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 // 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 // )
 
@@ -113,11 +113,11 @@ var _notavail = encodeValues(0, 30000, false)
 // 		// in_matrix := false
 // 		x1 := y - lB + extra
 // 		x2 := extra - y
-// 		xs := goutils.MaxInt(goutils.MaxInt(x1, x2), 0)
+// 		xs := obiutils.MaxInt(obiutils.MaxInt(x1, x2), 0)
 
 // 		x1 = y + extra
 // 		x2 = lA + extra - y
-// 		xf := goutils.MinInt(goutils.MinInt(x1, x2), even-1) + 1
+// 		xf := obiutils.MinInt(obiutils.MinInt(x1, x2), even-1) + 1
 
 // 		for x := xs; x < xf; x++ {
 
@@ -174,11 +174,11 @@ var _notavail = encodeValues(0, 30000, false)
 // 		// . 9   10 + 2 - 1
 // 		x1 = y - lB + extra + even
 // 		x2 = extra - y + even - 1
-// 		xs = goutils.MaxInt(goutils.MaxInt(x1, x2), even)
+// 		xs = obiutils.MaxInt(obiutils.MaxInt(x1, x2), even)
 
 // 		x1 = y + extra + even
 // 		x2 = lA + extra - y + even - 1
-// 		xf = goutils.MinInt(goutils.MinInt(x1, x2), width-1) + 1
+// 		xf = obiutils.MinInt(obiutils.MinInt(x1, x2), width-1) + 1
 
 // 		for x := xs; x < xf; x++ {
 

pkg/obialign/fastlcsegf.go

@@ -1,8 +1,8 @@
 package obialign
 
 import (
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 	log "github.com/sirupsen/logrus"
 )
 
@@ -109,11 +109,11 @@ func FastLCSEGFScoreByte(bA, bB []byte, maxError int, endgapfree bool, buffer *[
 		// in_matrix := false
 		x1 := y - lB + extra
 		x2 := extra - y
-		xs := goutils.MaxInt(goutils.MaxInt(x1, x2), 0)
+		xs := obiutils.MaxInt(obiutils.MaxInt(x1, x2), 0)
 
 		x1 = y + extra
 		x2 = lA + extra - y
-		xf := goutils.MinInt(goutils.MinInt(x1, x2), even-1) + 1
+		xf := obiutils.MinInt(obiutils.MinInt(x1, x2), even-1) + 1
 
 		for x := xs; x < xf; x++ {
 
@@ -201,11 +201,11 @@ func FastLCSEGFScoreByte(bA, bB []byte, maxError int, endgapfree bool, buffer *[
 		// . 9   10 + 2 - 1
 		x1 = y - lB + extra + even
 		x2 = extra - y + even - 1
-		xs = goutils.MaxInt(goutils.MaxInt(x1, x2), even)
+		xs = obiutils.MaxInt(obiutils.MaxInt(x1, x2), even)
 
 		x1 = y + extra + even
 		x2 = lA + extra - y + even - 1
-		xf = goutils.MinInt(goutils.MinInt(x1, x2), width-1) + 1
+		xf = obiutils.MinInt(obiutils.MinInt(x1, x2), width-1) + 1
 
 		for x := xs; x < xf; x++ {
 

pkg/obiapat/pattern.go

@@ -13,9 +13,9 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 )
 
 var _MaxPatLen = int(C.MAX_PAT_LEN)
@@ -355,8 +355,8 @@ func (pattern ApatPattern) BestMatch(sequence ApatSequence, begin, length int) (
 
 	start = best[0] - nerr
 	end = best[0] + int(pattern.pointer.pointer.patlen) + nerr
-	start = goutils.MaxInt(start, 0)
+	start = obiutils.MaxInt(start, 0)
-	end = goutils.MinInt(end, sequence.Len())
+	end = obiutils.MinInt(end, sequence.Len())
 
 	cpattern := (*[1 << 30]byte)(unsafe.Pointer(pattern.pointer.pointer.cpat))
 	cseq := (*[1 << 30]byte)(unsafe.Pointer(sequence.pointer.pointer.cseq))
@@ -374,7 +374,7 @@ func (pattern ApatPattern) BestMatch(sequence ApatSequence, begin, length int) (
 
 	nerr = lali - score
 	start = best[0] + int(pattern.pointer.pointer.patlen) - lali
-	end = start + lali 
+	end = start + lali
 	log.Debugln("results", score, lali, start, nerr)
 	return
 }

pkg/obiapat/pcr.go

@@ -3,8 +3,8 @@ package obiapat
 import (
 	log "github.com/sirupsen/logrus"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 )
 
 type _Options struct {
@@ -210,7 +210,7 @@ func _Pcr(seq ApatSequence,
 	reverse := opt.pointer.reverse
 	crev := opt.pointer.crev
 
-	forwardMatches := forward.FindAllIndex(seq,0,-1)
+	forwardMatches := forward.FindAllIndex(seq, 0, -1)
 
 	if len(forwardMatches) > 0 {
 
@@ -256,7 +256,7 @@ func _Pcr(seq ApatSequence,
 								(opt.MaxLength() == 0 || length <= opt.MaxLength()) {
 								amplicon, _ := sequence.Subsequence(fm[1], rm[0], opt.pointer.circular)
 								annot := amplicon.Annotations()
-								goutils.MustFillMap(annot, sequence.Annotations())
+								obiutils.MustFillMap(annot, sequence.Annotations())
 								annot["forward_primer"] = forward.String()
 
 								match, _ := sequence.Subsequence(fm[0], fm[1], opt.pointer.circular)
@@ -284,7 +284,7 @@ func _Pcr(seq ApatSequence,
 		}
 	}
 
-	forwardMatches = reverse.FindAllIndex(seq,0,-1)
+	forwardMatches = reverse.FindAllIndex(seq, 0, -1)
 	if forwardMatches != nil {
 
 		begin := forwardMatches[0][0]
@@ -331,7 +331,7 @@ func _Pcr(seq ApatSequence,
 								amplicon = amplicon.ReverseComplement(true)
 
 								annot := amplicon.Annotations()
-								goutils.MustFillMap(annot, sequence.Annotations())
+								obiutils.MustFillMap(annot, sequence.Annotations())
 								annot["forward_primer"] = forward.String()
 
 								match, _ := sequence.Subsequence(rm[0], rm[1], opt.pointer.circular)

pkg/obiformats/batch_of_files_reader.go

@@ -3,8 +3,8 @@ package obiformats
 import (
 	"log"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 )
 
 func ReadSequencesBatchFromFiles(filenames []string,
@@ -17,7 +17,7 @@ func ReadSequencesBatchFromFiles(filenames []string,
 	}
 
 	batchiter := obiiter.MakeIBioSequence(0)
-	nextCounter := goutils.AtomicCounter()
+	nextCounter := obiutils.AtomicCounter()
 
 	batchiter.Add(concurrent_readers)
 

pkg/obiformats/csv_writer.go

@@ -9,9 +9,9 @@ import (
 	"sync"
 	"time"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 	log "github.com/sirupsen/logrus"
 )
 
@@ -52,7 +52,7 @@ func CSVRecord(sequence *obiseq.BioSequence, opt Options) []string {
 			value = opt.CSVNAValue()
 		}
 
-		svalue, _ := goutils.InterfaceToString(value)
+		svalue, _ := obiutils.InterfaceToString(value)
 		record = append(record, svalue)
 	}
 
@@ -132,7 +132,7 @@ func WriteCSV(iterator obiiter.IBioSequence,
 	options ...WithOption) (obiiter.IBioSequence, error) {
 	opt := MakeOptions(options)
 
-	file, _ = goutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
+	file, _ = obiutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
 
 	newIter := obiiter.MakeIBioSequence()
 

pkg/obiformats/fastseq_json_header.go

@@ -6,8 +6,8 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 	"github.com/goccy/go-json"
 )
 
@@ -71,7 +71,7 @@ func FormatFastSeqJsonHeader(sequence *obiseq.BioSequence) string {
 	annotations := sequence.Annotations()
 
 	if len(annotations) > 0 {
-		text, err := goutils.JsonMarshal(sequence.Annotations())
+		text, err := obiutils.JsonMarshal(sequence.Annotations())
 
 		if err != nil {
 			panic(err)

pkg/obiformats/fastseq_obi_header.go

@@ -9,8 +9,8 @@ import (
 	"strconv"
 	"strings"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 	"github.com/goccy/go-json"
 )
 
@@ -305,7 +305,7 @@ func FormatFastSeqOBIHeader(sequence *obiseq.BioSequence) string {
 				map[string]string,
 				map[string]interface{},
 				obiseq.StatsOnValues:
-				tv, err := goutils.JsonMarshal(t)
+				tv, err := obiutils.JsonMarshal(t)
 				if err != nil {
 					log.Fatalf("Cannot convert %v value", value)
 				}

pkg/obiformats/fastseq_write_fasta.go

@@ -11,9 +11,9 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 )
 
 func min(x, y int) int {
@@ -70,7 +70,7 @@ func WriteFasta(iterator obiiter.IBioSequence,
 	opt := MakeOptions(options)
 
 	iterator = iterator.Rebatch(10000)
-	file, _ = goutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
+	file, _ = obiutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
 
 	newIter := obiiter.MakeIBioSequence()
 

pkg/obiformats/fastseq_write_fastq.go

@@ -10,9 +10,9 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 )
 
 func FormatFastq(seq *obiseq.BioSequence, quality_shift int, formater FormatHeader) string {
@@ -61,7 +61,7 @@ func WriteFastq(iterator obiiter.IBioSequence,
 
 	opt := MakeOptions(options)
 
-	file, _ = goutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
+	file, _ = obiutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
 
 	newIter := obiiter.MakeIBioSequence()
 

pkg/obiiter/batchiterator.go

@@ -10,8 +10,8 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 	"github.com/tevino/abool/v2"
 )
 
@@ -375,7 +375,7 @@ func (iterator IBioSequence) Pool(iterators ...IBioSequence) IBioSequence {
 		allPaired = allPaired && i.IsPaired()
 	}
 
-	nextCounter := goutils.AtomicCounter()
+	nextCounter := obiutils.AtomicCounter()
 	newIter := MakeIBioSequence()
 
 	newIter.Add(niterator)

pkg/obiiter/sequence_workers.go

@@ -2,7 +2,7 @@ package obiiter
 
 // func MakeSetAttributeWorker(rank string) obiiter.SeqWorker {
 
-// 	if !goutils.Contains(taxonomy.RankList(), rank) {
+// 	if !obiutils.Contains(taxonomy.RankList(), rank) {
 // 		log.Fatalf("%s is not a valid rank (allowed ranks are %v)",
 // 			rank,
 // 			taxonomy.RankList())
@@ -14,4 +14,4 @@ package obiiter
 // 	}
 
 // 	return w
-// }
+// }

pkg/obikmer/counting.go

@@ -3,8 +3,8 @@ package obikmer
 import (
 	"math"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 )
 
 type Table4mer [256]uint16
@@ -32,7 +32,7 @@ func Count4Mer(seq *obiseq.BioSequence, buffer *[]byte, counts *Table4mer) *Tabl
 func Common4Mer(count1, count2 *Table4mer) int {
 	sum := 0
 	for i := 0; i < 256; i++ {
-		sum += int(goutils.MinUInt16((*count1)[i], (*count2)[i]))
+		sum += int(obiutils.MinUInt16((*count1)[i], (*count2)[i]))
 	}
 	return sum
 }
@@ -48,7 +48,7 @@ func Sum4Mer(count *Table4mer) int {
 func LCS4MerBounds(count1, count2 *Table4mer) (int, int) {
 	s1 := Sum4Mer(count1)
 	s2 := Sum4Mer(count2)
-	smin := goutils.MinInt(s1, s2)
+	smin := obiutils.MinInt(s1, s2)
 
 	cw := Common4Mer(count1, count2)
 
@@ -65,11 +65,11 @@ func LCS4MerBounds(count1, count2 *Table4mer) (int, int) {
 func Error4MerBounds(count1, count2 *Table4mer) (int, int) {
 	s1 := Sum4Mer(count1)
 	s2 := Sum4Mer(count2)
-	smax := goutils.MaxInt(s1, s2)
+	smax := obiutils.MaxInt(s1, s2)
 
 	cw := Common4Mer(count1, count2)
 
-	errorMax := smax - cw + 2* int(math.Floor(float64(cw+5)/8.0))
+	errorMax := smax - cw + 2*int(math.Floor(float64(cw+5)/8.0))
 	errorMin := int(math.Ceil(float64(errorMax) / 4.0))
 
 	return errorMin, errorMax

pkg/obingslibrary/match.go

@@ -7,9 +7,9 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 )
 
 type DemultiplexMatch struct {
@@ -104,16 +104,14 @@ func (marker *Marker) Compile(forward, reverse string, maxError int, allowsIndel
 	return nil
 }
 
-
-
 func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
 	aseq, _ := obiapat.MakeApatSequence(sequence, false)
 
-	start, end, nerr ,matched := marker.forward.BestMatch(aseq, marker.taglength,-1)
+	start, end, nerr, matched := marker.forward.BestMatch(aseq, marker.taglength, -1)
 	if matched {
 		sseq := sequence.String()
 		direct := sseq[start:end]
-		tagstart := goutils.MaxInt(start - marker.taglength,0)
+		tagstart := obiutils.MaxInt(start-marker.taglength, 0)
 		ftag := strings.ToLower(sseq[tagstart:start])
 
 		m := DemultiplexMatch{
@@ -125,15 +123,15 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
 			Error:             nil,
 		}
 
-		start, end, nerr ,matched = marker.creverse.BestMatch(aseq, start,-1)
+		start, end, nerr, matched = marker.creverse.BestMatch(aseq, start, -1)
 
 		if matched {
 
 			// extracting primer matches
-			reverse, _ := sequence.Subsequence(start,end, false)
+			reverse, _ := sequence.Subsequence(start, end, false)
 			defer reverse.Recycle()
 			reverse = reverse.ReverseComplement(true)
-			endtag := goutils.MinInt(end+marker.taglength,sequence.Len())
+			endtag := obiutils.MinInt(end+marker.taglength, sequence.Len())
 			rtag, err := sequence.Subsequence(end, endtag, false)
 			defer rtag.Recycle()
 			srtag := ""
@@ -165,14 +163,13 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
 		return &m
 	}
 
-
+	start, end, nerr, matched = marker.reverse.BestMatch(aseq, marker.taglength, -1)
-	start, end, nerr ,matched = marker.reverse.BestMatch(aseq, marker.taglength,-1)
 
 	if matched {
 		sseq := sequence.String()
 
 		reverse := strings.ToLower(sseq[start:end])
-		tagstart := goutils.MaxInt(start - marker.taglength,0)
+		tagstart := obiutils.MaxInt(start-marker.taglength, 0)
 		rtag := strings.ToLower(sseq[tagstart:start])
 
 		m := DemultiplexMatch{
@@ -184,16 +181,16 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
 			Error:             nil,
 		}
 
-		start, end, nerr ,matched = marker.cforward.BestMatch(aseq, end,-1)
+		start, end, nerr, matched = marker.cforward.BestMatch(aseq, end, -1)
 
 		if matched {
 
-			direct, _ := sequence.Subsequence(start,end, false)
+			direct, _ := sequence.Subsequence(start, end, false)
 			defer direct.Recycle()
 			direct = direct.ReverseComplement(true)
 
-			endtag := goutils.MinInt(end+marker.taglength,sequence.Len())
+			endtag := obiutils.MinInt(end+marker.taglength, sequence.Len())
-			ftag, err := sequence.Subsequence(end,endtag, false)
+			ftag, err := sequence.Subsequence(end, endtag, false)
 			defer ftag.Recycle()
 			sftag := ""
 			if err != nil {

pkg/obiseq/attributes.go

@@ -4,7 +4,7 @@ import (
 	"fmt"
 	"strconv"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 	log "github.com/sirupsen/logrus"
 )
 
@@ -17,6 +17,7 @@ func (s *BioSequence) HasAttribute(key string) bool {
 
 	return ok
 }
+
 // A method that returns the value of the key in the annotation map.
 func (s *BioSequence) GetAttribute(key string) (interface{}, bool) {
 	var val interface{}
@@ -43,7 +44,7 @@ func (s *BioSequence) GetIntAttribute(key string) (int, bool) {
 	v, ok := s.GetAttribute(key)
 
 	if ok {
-		val, err = goutils.InterfaceToInt(v)
+		val, err = obiutils.InterfaceToInt(v)
 		ok = err == nil
 	}
 
@@ -52,15 +53,15 @@ func (s *BioSequence) GetIntAttribute(key string) (int, bool) {
 
 // Deleting the key from the annotation map.
 func (s *BioSequence) DeleteAttribute(key string) {
-	delete(s.Annotations(),key)
+	delete(s.Annotations(), key)
 }
- 
+
 // Renaming the key in the annotation map.
 func (s *BioSequence) RenameAttribute(newName, oldName string) {
-	val,ok := s.GetAttribute(oldName)
+	val, ok := s.GetAttribute(oldName)
 
-	if (ok) {
+	if ok {
-		s.SetAttribute(newName,val)
+		s.SetAttribute(newName, val)
 		s.DeleteAttribute(oldName)
 	}
 }
@@ -73,14 +74,13 @@ func (s *BioSequence) GetNumericAttribute(key string) (float64, bool) {
 	v, ok := s.GetAttribute(key)
 
 	if ok {
-		val, err = goutils.InterfaceToFloat64(v)
+		val, err = obiutils.InterfaceToFloat64(v)
 		ok = err == nil
 	}
 
 	return val, ok
 }
 
-
 // A method that returns the value of the key in the annotation map.
 func (s *BioSequence) GetStringAttribute(key string) (string, bool) {
 	var val string
@@ -101,7 +101,7 @@ func (s *BioSequence) GetBoolAttribute(key string) (bool, bool) {
 	v, ok := s.GetAttribute(key)
 
 	if ok {
-		val, err = goutils.InterfaceToBool(v)
+		val, err = obiutils.InterfaceToBool(v)
 		ok = err == nil
 	}
 
@@ -115,7 +115,7 @@ func (s *BioSequence) GetIntMap(key string) (map[string]int, bool) {
 	v, ok := s.GetAttribute(key)
 
 	if ok {
-		val, err = goutils.InterfaceToIntMap(v)
+		val, err = obiutils.InterfaceToIntMap(v)
 		ok = err == nil
 	}
 
@@ -139,7 +139,6 @@ func (s *BioSequence) SetCount(count int) {
 	annot["count"] = count
 }
 
-
 // Returning the taxid of the sequence.
 func (s *BioSequence) Taxid() int {
 	taxid, ok := s.GetIntAttribute("taxid")
@@ -157,7 +156,6 @@ func (s *BioSequence) SetTaxid(taxid int) {
 	annot["taxid"] = taxid
 }
 
-
 func (s *BioSequence) OBITagRefIndex() map[int]string {
 
 	var val map[int]string
@@ -179,7 +177,7 @@ func (s *BioSequence) OBITagRefIndex() map[int]string {
 				log.Panicln(err)
 			}
 
-			val[score], err = goutils.InterfaceToString(v)
+			val[score], err = obiutils.InterfaceToString(v)
 			if err != nil {
 				log.Panicln(err)
 			}

pkg/obiseq/class.go

@@ -6,7 +6,7 @@ import (
 	"strconv"
 	"sync"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 	log "github.com/sirupsen/logrus"
 )
 
@@ -135,7 +135,7 @@ func DualAnnotationClassifier(key1, key2 string, na string) *BioSequenceClassifi
 		locke.Lock()
 		defer locke.Unlock()
 
-		jb, _ := goutils.JsonMarshal([2]string{val1, val2})
+		jb, _ := obiutils.JsonMarshal([2]string{val1, val2})
 		json := string(jb)
 		k, ok := encode[json]
 

pkg/obiseq/language.go

@@ -5,7 +5,7 @@ import (
 	"log"
 	"strings"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 	"github.com/PaesslerAG/gval"
 )
 
@@ -136,11 +136,11 @@ func minFloatMap(values map[string]float64) float64 {
 var OBILang = gval.NewLanguage(
 	gval.Full(),
 	gval.Function("len", func(args ...interface{}) (interface{}, error) {
-		length := goutils.Len(args[0])
+		length := obiutils.Len(args[0])
 		return (float64)(length), nil
 	}),
 	gval.Function("ismap", func(args ...interface{}) (interface{}, error) {
-		ismap := goutils.IsAMap(args[0])
+		ismap := obiutils.IsAMap(args[0])
 		return ismap, nil
 	}),
 	gval.Function("printf", func(args ...interface{}) (interface{}, error) {
@@ -152,7 +152,7 @@ var OBILang = gval.NewLanguage(
 		return text, nil
 	}),
 	gval.Function("int", func(args ...interface{}) (interface{}, error) {
-		val, err := goutils.InterfaceToInt(args[0])
+		val, err := obiutils.InterfaceToInt(args[0])
 
 		if err != nil {
 			log.Fatalf("%v cannot be converted to an integer value", args[0])
@@ -160,7 +160,7 @@ var OBILang = gval.NewLanguage(
 		return val, nil
 	}),
 	gval.Function("numeric", func(args ...interface{}) (interface{}, error) {
-		val, err := goutils.InterfaceToFloat64(args[0])
+		val, err := obiutils.InterfaceToFloat64(args[0])
 
 		if err != nil {
 			log.Fatalf("%v cannot be converted to a numeric value", args[0])
@@ -168,7 +168,7 @@ var OBILang = gval.NewLanguage(
 		return val, nil
 	}),
 	gval.Function("bool", func(args ...interface{}) (interface{}, error) {
-		val, err := goutils.InterfaceToBool(args[0])
+		val, err := obiutils.InterfaceToBool(args[0])
 
 		if err != nil {
 			log.Fatalf("%v cannot be converted to a boolan value", args[0])
@@ -189,4 +189,3 @@ var OBILang = gval.NewLanguage(
 	gval.Function("composition", func(args ...interface{}) (interface{}, error) {
 		return (args[0].(*BioSequence)).Composition(), nil
 	}))
-

pkg/obiseq/merge.go

@@ -5,7 +5,7 @@ import (
 	"reflect"
 	"strings"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 	log "github.com/sirupsen/logrus"
 )
 
@@ -53,7 +53,7 @@ func (sequence *BioSequence) StatsOn(key string, na string) StatsOnValues {
 			newstat = false
 			var err error
 			for k, v := range istat {
-				stats[k], err = goutils.InterfaceToInt(v)
+				stats[k], err = obiutils.InterfaceToInt(v)
 				if err != nil {
 					log.Panicf("In sequence %s : %s stat tag not only containing integer values %s",
 						sequence.Id(), mkey, istat)

pkg/obiseq/pool.go

@@ -4,7 +4,7 @@ import (
 	"log"
 	"sync"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 )
 
 var _BioSequenceByteSlicePool = sync.Pool{
@@ -72,7 +72,7 @@ func GetAnnotation(values ...Annotation) Annotation {
 	}
 
 	if len(values) > 0 {
-		goutils.MustFillMap(a, values[0])
+		obiutils.MustFillMap(a, values[0])
 	}
 
 	return a

pkg/obitax/sequence_predicate.go

@@ -3,8 +3,8 @@ package obitax
 import (
 	log "github.com/sirupsen/logrus"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 )
 
 func (taxonomy *Taxonomy) IsAValidTaxon(withAutoCorrection ...bool) obiseq.SequencePredicate {
@@ -59,7 +59,7 @@ func (taxonomy *Taxonomy) IsSubCladeOf(taxid int) obiseq.SequencePredicate {
 
 func (taxonomy *Taxonomy) HasRequiredRank(rank string) obiseq.SequencePredicate {
 
-	if !goutils.Contains(taxonomy.RankList(), rank) {
+	if !obiutils.Contains(taxonomy.RankList(), rank) {
 		log.Fatalf("%s is not a valid rank (allowed ranks are %v)",
 			rank,
 			taxonomy.RankList())

pkg/obitax/sequence_workers.go

@@ -1,14 +1,14 @@
 package obitax
 
 import (
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 	log "github.com/sirupsen/logrus"
 )
 
 func (taxonomy *Taxonomy) MakeSetTaxonAtRankWorker(rank string) obiseq.SeqWorker {
 
-	if !goutils.Contains(taxonomy.RankList(), rank) {
+	if !obiutils.Contains(taxonomy.RankList(), rank) {
 		log.Fatalf("%s is not a valid rank (allowed ranks are %v)",
 			rank,
 			taxonomy.RankList())

pkg/obitools/obiclean/obiclean.go

@@ -4,10 +4,10 @@ import (
 	"fmt"
 	"os"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 	"github.com/schollz/progressbar/v3"
 	log "github.com/sirupsen/logrus"
 )
@@ -120,7 +120,7 @@ func HeadCount(sequence *obiseq.BioSequence) int {
 	value := 0
 
 	if ok {
-		value, err = goutils.InterfaceToInt(value)
+		value, err = obiutils.InterfaceToInt(value)
 		if err != nil {
 			log.Panic("obiclean_headcount attribute of sequence %s must be an integer value not : %v", sequence.Id(), ivalue)
 		}
@@ -136,7 +136,7 @@ func InternalCount(sequence *obiseq.BioSequence) int {
 	value := 0
 
 	if ok {
-		value, err = goutils.InterfaceToInt(value)
+		value, err = obiutils.InterfaceToInt(value)
 		if err != nil {
 			log.Panic("obiclean_internalcount attribute of sequence %s must be an integer value not : %v", sequence.Id(), ivalue)
 		}
@@ -152,7 +152,7 @@ func SingletonCount(sequence *obiseq.BioSequence) int {
 	value := 0
 
 	if ok {
-		value, err = goutils.InterfaceToInt(value)
+		value, err = obiutils.InterfaceToInt(value)
 		if err != nil {
 			log.Panic("obiclean_samplecount attribute of sequence %s must be an integer value not : %v", sequence.Id(), ivalue)
 		}
@@ -271,7 +271,7 @@ func Weight(sequence *obiseq.BioSequence) map[string]int {
 		case map[string]interface{}:
 			weight = make(map[string]int)
 			for k, v := range iobistatus {
-				weight[k], err = goutils.InterfaceToInt(v)
+				weight[k], err = obiutils.InterfaceToInt(v)
 				if err != nil {
 					log.Panicf("Weight value %v cannnot be casted to an integer value\n", v)
 				}

pkg/obitools/obicsv/options.go

@@ -1,8 +1,8 @@
 package obicsv
 
 import (
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 	"github.com/DavidGamba/go-getoptions"
 )
 
@@ -103,18 +103,18 @@ func CLIToBeKeptAttributes() []string {
 		_keepOnly = append(_keepOnly, _softAttributes["obipairing"]...)
 	}
 
-	if i := goutils.LookFor(_keepOnly, "count"); i >= 0 {
+	if i := obiutils.LookFor(_keepOnly, "count"); i >= 0 {
-		_keepOnly = goutils.RemoveIndex(_keepOnly, i)
+		_keepOnly = obiutils.RemoveIndex(_keepOnly, i)
 		_outputCount = true
 	}
 
-	if i := goutils.LookFor(_keepOnly, "taxid"); i >= 0 {
+	if i := obiutils.LookFor(_keepOnly, "taxid"); i >= 0 {
-		_keepOnly = goutils.RemoveIndex(_keepOnly, i)
+		_keepOnly = obiutils.RemoveIndex(_keepOnly, i)
 		_outputTaxon = true
 	}
 
-	if i := goutils.LookFor(_keepOnly, "scientific_name"); i >= 0 {
+	if i := obiutils.LookFor(_keepOnly, "scientific_name"); i >= 0 {
-		_keepOnly = goutils.RemoveIndex(_keepOnly, i)
+		_keepOnly = obiutils.RemoveIndex(_keepOnly, i)
 		_outputTaxon = true
 	}
 

pkg/obitools/obigrep/options.go

@@ -5,11 +5,11 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats/ncbitaxdump"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 	"github.com/DavidGamba/go-getoptions"
 )
 
@@ -345,7 +345,7 @@ func CLIIdPatternPredicate() obiseq.SequencePredicate {
 func CLIIdListPredicate() obiseq.SequencePredicate {
 
 	if _IdList != "" {
-		ids, err := goutils.ReadLines(_IdList)
+		ids, err := obiutils.ReadLines(_IdList)
 
 		if err != nil {
 			log.Fatalf("cannot read the id file %s : %v", _IdList, err)

pkg/obitools/obirefidx/obirefidx.go

@@ -5,7 +5,6 @@ import (
 	"log"
 	"os"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obikmer"
@@ -13,6 +12,7 @@ import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obifind"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 	"github.com/schollz/progressbar/v3"
 )
 
@@ -38,7 +38,7 @@ func IndexSequence(seqidx int,
 
 	// log.Println("Redone : ",r,"/",t,"(",w,")")
 
-	o := goutils.IntOrder(score)
+	o := obiutils.IntOrder(score)
 
 	current_taxid, err := taxo.Taxon(references[o[0]].Taxid())
 	current_score := score[o[0]]
@@ -121,7 +121,7 @@ func IndexReferenceDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 	indexed := obiiter.MakeIBioSequence()
 	go func() {
 		for i := 0; i < len(references); i += 10 {
-			limits <- [2]int{i, goutils.MinInt(i+10, len(references))}
+			limits <- [2]int{i, obiutils.MinInt(i+10, len(references))}
 		}
 		close(limits)
 	}()

pkg/obitools/obitag/obitag.go

@@ -6,7 +6,6 @@ import (
 	"strconv"
 	"strings"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obikmer"
@@ -15,6 +14,7 @@ import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obifind"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obirefidx"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 )
 
 func FindClosests(sequence *obiseq.BioSequence,
@@ -31,7 +31,7 @@ func FindClosests(sequence *obiseq.BioSequence,
 		cw[i] = obikmer.Common4Mer(seqwords, ref)
 	}
 
-	o := goutils.ReverseIntOrder(cw)
+	o := obiutils.ReverseIntOrder(cw)
 
 	// mcw := 100000
 	// for _, i := range o {
@@ -57,11 +57,11 @@ func FindClosests(sequence *obiseq.BioSequence,
 	for i, j := range o {
 		ref := references[j]
 
-		lmin, lmax := goutils.MinMaxInt(sequence.Len(), ref.Len())
+		lmin, lmax := obiutils.MinMaxInt(sequence.Len(), ref.Len())
 		atMost := lmax - lmin + int(math.Ceil(float64(lmin-3-cw[j])/4.0)) - 2
 
 		if i == 0 {
-			maxe = goutils.MaxInt(sequence.Len(), ref.Len())
+			maxe = obiutils.MaxInt(sequence.Len(), ref.Len())
 		}
 
 		// log.Println(sequence.Id(),cw[j], maxe)

pkg/obiutils/goutils.go

@@ -1,4 +1,4 @@
-package goutils
+package obiutils
 
 import (
 	"bufio"
@@ -13,7 +13,6 @@ import (
 	"github.com/barkimedes/go-deepcopy"
 )
 
-
 // InterfaceToInt converts a interface{} to an integer value if possible.
 // If not a "NotAnInteger" error is returned via the err
 // return value and val is set to 0.
@@ -197,7 +196,6 @@ func InterfaceToFloat64Map(i interface{}) (val map[string]float64, err error) {
 	return
 }
 
-
 // NotABoolean defines a new type of Error : "NotABoolean"
 type NotABoolean struct {
 	message string

pkg/obiutils/gzipfile.go

@@ -1,4 +1,4 @@
-package goutils
+package obiutils
 
 import (
 	"bufio"

pkg/obiutils/minmax.go

@@ -0,0 +1,83 @@
+package obiutils
+
+import "golang.org/x/exp/constraints"
+
+func MinInt(x, y int) int {
+	if x < y {
+		return x
+	}
+	return y
+}
+
+func MaxInt(x, y int) int {
+	if x < y {
+		return y
+	}
+	return x
+}
+
+func MinMaxInt(x, y int) (int, int) {
+	if x < y {
+		return x, y
+	}
+	return y, x
+}
+
+func MinUInt16(x, y uint16) uint16 {
+	if x < y {
+		return x
+	}
+	return y
+}
+
+func MaxUInt16(x, y uint16) uint16 {
+	if x < y {
+		return y
+	}
+	return x
+}
+
+func MinSlice[T constraints.Ordered](vec []T) T {
+	if len(vec) == 0 {
+		panic("empty slice")
+	}
+	min := vec[0]
+	for _, v := range vec {
+		if v < min {
+			min = v
+		}
+	}
+	return min
+}
+
+func MaxSlice[T constraints.Ordered](vec []T) T {
+	if len(vec) == 0 {
+		panic("empty slice")
+	}
+	max := vec[0]
+	for _, v := range vec {
+		if v > max {
+			max = v
+		}
+	}
+	return max
+}
+
+func RangeSlice[T constraints.Ordered](vec []T) (min, max T) {
+	if len(vec) == 0 {
+		panic("empty slice")
+	}
+
+	min = vec[0]
+	max = vec[0]
+	for _, v := range vec {
+		if v > max {
+			max = v
+		}
+		if v < min {
+			min = v
+		}
+	}
+
+	return
+}

pkg/obiutils/ranks.go

@@ -1,6 +1,8 @@
-package goutils
+package obiutils
 
-import "sort"
+import (
+	"sort"
+)
 
 // intRanker is a helper type for the rank function.
 type intRanker struct {
@@ -29,7 +31,7 @@ func IntOrder(data []int) []int {
 	}
 
 	sort.Sort(rk)
-	
+
 	return r
 }
 
@@ -49,6 +51,36 @@ func ReverseIntOrder(data []int) []int {
 	}
 
 	sort.Sort(sort.Reverse(rk))
-	
+
+	return r
+}
+
+type Ranker[T sort.Interface] struct {
+	x T     // Data to be ranked.
+	r []int // A list of indexes into f that reflects rank order after sorting.
+}
+
+// ranker satisfies the sort.Interface without mutating the reference slice, f.
+func (r Ranker[_]) Len() int           { return len(r.r) }
+func (r Ranker[T]) Less(i, j int) bool { return r.x.Less(r.r[i], r.r[j]) }
+func (r Ranker[_]) Swap(i, j int)      { r.r[i], r.r[j] = r.r[j], r.r[i] }
+
+func Order[T sort.Interface](data T) []int {
+	ldata := data.Len()
+	if ldata == 0 {
+		return nil
+	}
+	r := make([]int, ldata)
+	rk := Ranker[T]{
+		x: data,
+		r: r,
+	}
+
+	for i := 0; i < ldata; i++ {
+		rk.r[i] = i
+	}
+
+	sort.Sort(rk)
+
 	return r
 }

pkg/obiutils/slices.go

@@ -1,5 +1,4 @@
-package goutils
+package obiutils
-
 
 func Contains[T comparable](arr []T, x T) bool {
 	for _, v := range arr {
@@ -20,5 +19,5 @@ func LookFor[T comparable](arr []T, x T) int {
 }
 
 func RemoveIndex[T comparable](s []T, index int) []T {
-    return append(s[:index], s[index+1:]...)
+	return append(s[:index], s[index+1:]...)
 }