From dd9307a4cd277011e44c16c7ea4856b593565e1a Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Thu, 30 May 2024 08:27:24 +0200
Subject: [PATCH] Swich to the system min and max functions and remove the
 version from obiutils

Former-commit-id: 8c4558921b0d0c266b070f16e83813de6e6d4a0f
---
 pkg/obialign/fastlcsegf.go          | 10 ++--
 pkg/obiapat/pattern.go              | 53 +++++++++++++------
 pkg/obiformats/fastqseq_read.go     | 81 -----------------------------
 pkg/obiiter/fragment.go             |  3 +-
 pkg/obikmer/counting.go             |  9 ++--
 pkg/obikmer/debruijn.go             |  3 +-
 pkg/obingslibrary/match.go          |  9 ++--
 pkg/obisuffix/suffix_array.go       |  5 +-
 pkg/obitools/obipcr/pcr.go          |  5 +-
 pkg/obitools/obirefidx/obirefidx.go |  4 +-
 pkg/obitools/obitag/obitag.go       |  6 +--
 pkg/obiutils/minmax.go              | 15 ------
 12 files changed, 58 insertions(+), 145 deletions(-)

diff --git a/pkg/obialign/fastlcsegf.go b/pkg/obialign/fastlcsegf.go
index 152238b..c80414d 100644
--- a/pkg/obialign/fastlcsegf.go
+++ b/pkg/obialign/fastlcsegf.go
@@ -2,7 +2,6 @@ package obialign
 
 import (
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 var _iupac = [26]byte{
@@ -130,11 +129,11 @@ func FastLCSEGFScoreByte(bA, bB []byte, maxError int, endgapfree bool, buffer *[
 		// in_matrix := false
 		x1 := y - lB + extra
 		x2 := extra - y
-		xs := obiutils.Max(obiutils.Max(x1, x2), 0)
+		xs := max(x1, x2, 0)
 
 		x1 = y + extra
 		x2 = lA + extra - y
-		xf := obiutils.Min(obiutils.Min(x1, x2), even-1) + 1
+		xf := min(x1, x2, even-1) + 1
 
 		for x := xs; x < xf; x++ {
 
@@ -222,11 +221,11 @@ 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 = obiutils.Max(obiutils.Max(x1, x2), even)
+		xs = max(x1, x2, even)
 
 		x1 = y + extra + even
 		x2 = lA + extra - y + even - 1
-		xf = obiutils.Min(obiutils.Min(x1, x2), width-1) + 1
+		xf = min(x1, x2, width-1) + 1
 
 		for x := xs; x < xf; x++ {
 
@@ -383,4 +382,3 @@ func FastLCSEGFScore(seqA, seqB *obiseq.BioSequence, maxError int, buffer *[]uin
 func FastLCSScore(seqA, seqB *obiseq.BioSequence, maxError int, buffer *[]uint64) (int, int) {
 	return FastLCSEGFScoreByte(seqA.Sequence(), seqB.Sequence(), maxError, false, buffer)
 }
-
diff --git a/pkg/obiapat/pattern.go b/pkg/obiapat/pattern.go
index 7ee9555..fd5a050 100644
--- a/pkg/obiapat/pattern.go
+++ b/pkg/obiapat/pattern.go
@@ -15,7 +15,6 @@ import (
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 var _MaxPatLen = int(C.MAX_PAT_LEN)
@@ -53,26 +52,24 @@ var NilApatPattern = ApatPattern{nil}
 // type.
 var NilApatSequence = ApatSequence{nil}
 
-// MakeApatPattern creates an ApatPattern object based on the given pattern, error maximum and allowsIndel flag.
+// MakeApatPattern creates an ApatPattern object based on the given pattern, error maximum, and allowsIndel flag.
 //
-// The pattern is a short DNA sequence (up to 64 symboles).
+// Parameters:
+// The pattern is a short DNA sequence (up to 64 symbols).
 // Ambiguities can be represented or using UIPAC symboles,
 // or using the [...] classical in regular pattern grammar.
 // For example, the ambiguity A/T can be indicated using W
 // or [AT]. A nucleotide can be negated by preceding it with
-// a '!'. The APAT algorithm allows for error during the
-// matching process. The maximum number of tolerated error
-// is indicated at the construction of the pattern using
-// the errormax parameter. Some positions can be marked as not
+// a '!'. The pattern is converted to uppercase.
+// Some positions can be marked as not
 // allowed for mismatches. They have to be signaled using a '#'
 // sign after the corresponding nucleotide.
 //
-// Parameters:
-// pattern: The input pattern string.
-// errormax: The maximum number of errors allowed.
-// allowsIndel: A flag indicating whether indels are allowed or not.
+// errormax is the maximum number of errors allowed in the pattern.
 //
-// Returns an ApatPattern object and an error.
+// allowsIndel is a flag indicating whether indels are allowed in the pattern.
+//
+// Returns an ApatPattern object and an error if the pattern is invalid.
 func MakeApatPattern(pattern string, errormax int, allowsIndel bool) (ApatPattern, error) {
 	cpattern := C.CString(pattern)
 	defer C.free(unsafe.Pointer(cpattern))
@@ -264,6 +261,7 @@ func (sequence ApatSequence) Free() {
 // values of the [3]int indicate respectively the start and the end position of
 // the match. Following the GO convention the end position is not included in the
 // match. The third value indicates the number of error detected for this occurrence.
+
 func (pattern ApatPattern) FindAllIndex(sequence ApatSequence, begin, length int) (loc [][3]int) {
 	if begin < 0 {
 		begin = 0
@@ -348,8 +346,8 @@ func (pattern ApatPattern) BestMatch(sequence ApatSequence, begin, length int) (
 
 	start = best[0] - nerr
 	end = best[0] + int(pattern.pointer.pointer.patlen) + nerr
-	start = obiutils.Max(start, 0)
-	end = obiutils.Min(end, sequence.Len())
+	start = max(start, 0)
+	end = min(end, sequence.Len())
 
 	cpattern := (*[1 << 30]byte)(unsafe.Pointer(pattern.pointer.pointer.cpat))
 	frg := sequence.pointer.reference.Sequence()[start:end]
@@ -377,6 +375,22 @@ func (pattern ApatPattern) BestMatch(sequence ApatSequence, begin, length int) (
 // 	return int(_AllocatedApaSequences)
 // }
 
+// AllMatches finds all matches of a given pattern in a sequence.
+//
+// It only works if the parttern is a pure IUPAC sequence without
+// supplementary characters normally allowed : ! and #.
+//
+// It takes the following parameters:
+// - pattern: the pattern to search for (ApatPattern).
+// - sequence: the sequence to search in (ApatSequence).
+// - begin: the starting index of the search (int).
+// - length: the length of the search (int).
+//
+// It returns a slice of [3]int representing the locations of all matches in the sequence.
+// The AllMatches methood returns return a slice of [3]int. The two firsts
+// values of the [3]int indicate respectively the start and the end position of
+// the match. Following the GO convention the end position is not included in the
+// match. The third value indicates the number of error detected for this occurrence.
 func (pattern ApatPattern) AllMatches(sequence ApatSequence, begin, length int) (loc [][3]int) {
 	res := pattern.FindAllIndex(sequence, begin, length)
 
@@ -384,12 +398,17 @@ func (pattern ApatPattern) AllMatches(sequence ApatSequence, begin, length int)
 	buffer := sbuffer[:]
 
 	for _, m := range res {
+		// Recompute the start and end position of the match
+		// when the pattern allows for indels
 		if m[2] > 0 && pattern.pointer.pointer.hasIndel {
 			start := m[0] - m[2]
 			end := m[0] + int(pattern.pointer.pointer.patlen) + m[2]
-			start = obiutils.Max(start, 0)
-			end = obiutils.Min(end, sequence.Len())
-
+			start = max(start, 0)
+			end = min(end, sequence.Len())
+			// 1 << 30 = 1,073,741,824 = 1Gb
+			// It's a virtual array mapping the sequence to the pattern
+			// in the C code.
+			// No allocations are done here.
 			cpattern := (*[1 << 30]byte)(unsafe.Pointer(pattern.pointer.pointer.cpat))
 			frg := sequence.pointer.reference.Sequence()[start:end]
 
diff --git a/pkg/obiformats/fastqseq_read.go b/pkg/obiformats/fastqseq_read.go
index 6437ad8..67ed182 100644
--- a/pkg/obiformats/fastqseq_read.go
+++ b/pkg/obiformats/fastqseq_read.go
@@ -100,87 +100,6 @@ func _EndOfLastFastqEntry(buffer []byte) int {
 	return cut
 }
 
-func lastFastqCut(buffer []byte) ([]byte, []byte) {
-	imax := len(buffer)
-	cut := imax
-	state := 0
-	restart := imax - 1
-	for i := restart; i >= 0 && state < 7; i-- {
-		C := buffer[i]
-		is_end_of_line := C == '\r' || C == '\n'
-		is_space := C == ' ' || C == '\t'
-		is_sep := is_space || is_end_of_line
-
-		switch state {
-		case 0:
-			if C == '+' {
-				// Potential start of quality part step 1
-				state = 1
-				restart = i
-			}
-		case 1:
-			if is_end_of_line {
-				// Potential start of quality part step 2
-				state = 2
-			} else {
-				// it was not the start of quality part
-				state = 0
-				i = restart
-			}
-		case 2:
-			if is_sep {
-				// Potential start of quality part step 2 (stay in the same state)
-				state = 2
-			} else if (C >= 'a' && C <= 'z') || (C >= 'A' && C <= 'Z') || C == '-' || C == '.' || C == '[' || C == ']' {
-				// End of the sequence
-				state = 3
-			} else {
-				// it was not the start of quality part
-				state = 0
-				i = restart
-			}
-		case 3:
-			if is_end_of_line {
-				// Entrering in the header line
-				state = 4
-			} else if (C >= 'a' && C <= 'z') || (C >= 'A' && C <= 'Z') || C == '-' || C == '.' || C == '[' || C == ']' {
-				// progressing along of the sequence
-				state = 3
-			} else {
-				// it was not the sequence part
-				state = 0
-				i = restart
-			}
-		case 4:
-			if is_end_of_line {
-				state = 4
-			} else {
-				state = 5
-			}
-		case 5:
-			if is_end_of_line {
-				// It was not the header line
-				state = 0
-				i = restart
-			} else if C == '@' {
-				state = 6
-				cut = i
-			}
-		case 6:
-			if is_end_of_line {
-				state = 7
-			} else {
-				state = 0
-				i = restart
-			}
-		}
-	}
-	if state == 7 {
-		return buffer[:cut], bytes.Clone(buffer[cut:])
-	}
-	return []byte{}, buffer
-}
-
 func _ParseFastqFile(source string,
 	input ChannelSeqFileChunk,
 	out obiiter.IBioSequence,
diff --git a/pkg/obiiter/fragment.go b/pkg/obiiter/fragment.go
index 7abdd6b..bbddd23 100644
--- a/pkg/obiiter/fragment.go
+++ b/pkg/obiiter/fragment.go
@@ -4,7 +4,6 @@ import (
 	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 func IFragments(minsize, length, overlap, size, nworkers int) Pipeable {
@@ -30,7 +29,7 @@ func IFragments(minsize, length, overlap, size, nworkers int) Pipeable {
 						news = append(news, s)
 					} else {
 						for i := 0; i < s.Len(); i += step {
-							end := obiutils.Min(i+length, s.Len())
+							end := min(i+length, s.Len())
 							fusion := false
 							if (s.Len() - end) < step {
 								end = s.Len()
diff --git a/pkg/obikmer/counting.go b/pkg/obikmer/counting.go
index 5ce8d31..1c27967 100644
--- a/pkg/obikmer/counting.go
+++ b/pkg/obikmer/counting.go
@@ -4,13 +4,10 @@ import (
 	"math"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 type Table4mer [256]uint16
 
-
-
 func Count4Mer(seq *obiseq.BioSequence, buffer *[]byte, counts *Table4mer) *Table4mer {
 	iternal_buffer := Encode4mer(seq, buffer) // The slice of 4-mer codes
 
@@ -33,7 +30,7 @@ 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(obiutils.Min((*count1)[i], (*count2)[i]))
+		sum += int(min((*count1)[i], (*count2)[i]))
 	}
 	return sum
 }
@@ -49,7 +46,7 @@ func Sum4Mer(count *Table4mer) int {
 func LCS4MerBounds(count1, count2 *Table4mer) (int, int) {
 	s1 := Sum4Mer(count1)
 	s2 := Sum4Mer(count2)
-	smin := obiutils.Min(s1, s2)
+	smin := min(s1, s2)
 
 	cw := Common4Mer(count1, count2)
 
@@ -66,7 +63,7 @@ func LCS4MerBounds(count1, count2 *Table4mer) (int, int) {
 func Error4MerBounds(count1, count2 *Table4mer) (int, int) {
 	s1 := Sum4Mer(count1)
 	s2 := Sum4Mer(count2)
-	smax := obiutils.Max(s1, s2)
+	smax := max(s1, s2)
 
 	cw := Common4Mer(count1, count2)
 
diff --git a/pkg/obikmer/debruijn.go b/pkg/obikmer/debruijn.go
index 9ef8c6b..3bafddd 100644
--- a/pkg/obikmer/debruijn.go
+++ b/pkg/obikmer/debruijn.go
@@ -10,7 +10,6 @@ import (
 	"slices"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	log "github.com/sirupsen/logrus"
 )
 
@@ -472,7 +471,7 @@ func (graph *DeBruijnGraph) Gml() string {
 		n := graph.Nexts(idx)
 		for _, dst := range n {
 			dstid := nodeidx[dst]
-			weight := obiutils.Min(graph.Weight(dst), weight)
+			weight := min(graph.Weight(dst), weight)
 			label := decode[dst&3]
 			buffer.WriteString(
 				fmt.Sprintf(`edge [ source "%d"
diff --git a/pkg/obingslibrary/match.go b/pkg/obingslibrary/match.go
index 5621aed..68bd10e 100644
--- a/pkg/obingslibrary/match.go
+++ b/pkg/obingslibrary/match.go
@@ -9,7 +9,6 @@ import (
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiapat"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 type DemultiplexMatch struct {
@@ -130,7 +129,7 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
 
 		sseq := sequence.String()
 		direct := sseq[start:end]
-		tagstart := obiutils.Max(start-marker.taglength, 0)
+		tagstart := max(start-marker.taglength, 0)
 		ftag := strings.ToLower(sseq[tagstart:start])
 
 		m := DemultiplexMatch{
@@ -150,7 +149,7 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
 			reverse, _ := sequence.Subsequence(start, end, false)
 			defer reverse.Recycle()
 			reverse = reverse.ReverseComplement(true)
-			endtag := obiutils.Min(end+marker.taglength, sequence.Len())
+			endtag := min(end+marker.taglength, sequence.Len())
 			rtag, err := sequence.Subsequence(end, endtag, false)
 			defer rtag.Recycle()
 			srtag := ""
@@ -201,7 +200,7 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
 		sseq := sequence.String()
 
 		reverse := strings.ToLower(sseq[start:end])
-		tagstart := obiutils.Max(start-marker.taglength, 0)
+		tagstart := max(start-marker.taglength, 0)
 		rtag := strings.ToLower(sseq[tagstart:start])
 
 		m := DemultiplexMatch{
@@ -221,7 +220,7 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
 			defer direct.Recycle()
 			direct = direct.ReverseComplement(true)
 
-			endtag := obiutils.Min(end+marker.taglength, sequence.Len())
+			endtag := min(end+marker.taglength, sequence.Len())
 			ftag, err := sequence.Subsequence(end, endtag, false)
 			defer ftag.Recycle()
 			sftag := ""
diff --git a/pkg/obisuffix/suffix_array.go b/pkg/obisuffix/suffix_array.go
index cb28931..87927f7 100644
--- a/pkg/obisuffix/suffix_array.go
+++ b/pkg/obisuffix/suffix_array.go
@@ -6,7 +6,6 @@ import (
 	"sort"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 type Suffix struct {
@@ -27,7 +26,7 @@ func SuffixLess(suffixarray SuffixArray) func(i, j int) bool {
 		sj := suffixarray.Suffixes[j]
 		bj := (*suffixarray.Sequences)[int(sj.Idx)].Sequence()[sj.Pos:]
 
-		l := obiutils.Min(len(bi), len(bj))
+		l := min(len(bi), len(bj))
 		p := 0
 		for p < l && bi[p] == bj[p] {
 			p++
@@ -92,7 +91,7 @@ func (suffixarray *SuffixArray) CommonSuffix() []int {
 		si := suffixarray.Suffixes[i]
 		bi := (*suffixarray.Sequences)[int(si.Idx)].Sequence()[si.Pos:]
 
-		l := obiutils.Min(len(bi), len(bp))
+		l := min(len(bi), len(bp))
 		p := 0
 		for p < l && bi[p] == bp[p] {
 			p++
diff --git a/pkg/obitools/obipcr/pcr.go b/pkg/obitools/obipcr/pcr.go
index 3fbf18d..f713b76 100644
--- a/pkg/obitools/obipcr/pcr.go
+++ b/pkg/obitools/obipcr/pcr.go
@@ -4,7 +4,6 @@ import (
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiapat"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	log "github.com/sirupsen/logrus"
 )
 
@@ -47,8 +46,8 @@ func CLIPCR(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error) {
 		frags := obiiter.IFragments(
 			CLIMaxLength()*1000,
 			CLIMaxLength()*100,
-			CLIMaxLength()+obiutils.Max(len(CLIForwardPrimer()),
-				len(CLIReversePrimer()))+obiutils.Min(len(CLIForwardPrimer()),
+			CLIMaxLength()+max(len(CLIForwardPrimer()),
+				len(CLIReversePrimer()))+min(len(CLIForwardPrimer()),
 				len(CLIReversePrimer()))/2,
 			100,
 			obioptions.CLIParallelWorkers(),
diff --git a/pkg/obitools/obirefidx/obirefidx.go b/pkg/obitools/obirefidx/obirefidx.go
index 6509028..74fcb90 100644
--- a/pkg/obitools/obirefidx/obirefidx.go
+++ b/pkg/obitools/obirefidx/obirefidx.go
@@ -63,7 +63,7 @@ func IndexSequence(seqidx int,
 			if lca[order] == ancestor {
 				// nseq[i]++
 				if mini != -1 {
-					wordmin = obiutils.Max(sequence.Len(), references[order].Len()) - 3 - 4*mini
+					wordmin = max(sequence.Len(), references[order].Len()) - 3 - 4*mini
 				}
 
 				if cw[order] < wordmin {
@@ -189,7 +189,7 @@ func IndexReferenceDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 	indexed := obiiter.MakeIBioSequence()
 	go func() {
 		for i := 0; i < len(references); i += 10 {
-			limits <- [2]int{i, obiutils.Min(i+10, len(references))}
+			limits <- [2]int{i, min(i+10, len(references))}
 		}
 		close(limits)
 	}()
diff --git a/pkg/obitools/obitag/obitag.go b/pkg/obitools/obitag/obitag.go
index b4b8e84..5dd4db2 100644
--- a/pkg/obitools/obitag/obitag.go
+++ b/pkg/obitools/obitag/obitag.go
@@ -110,7 +110,7 @@ func FindClosests(sequence *obiseq.BioSequence,
 			d, _, _, _ := obialign.D1Or0(sequence, references[order])
 			if d >= 0 {
 				score = d
-				alilength = obiutils.Max(sequence.Len(), ref.Len())
+				alilength = max(sequence.Len(), ref.Len())
 				lcs = alilength - score
 			}
 		} else {
@@ -294,8 +294,8 @@ func CLIAssignTaxonomy(iterator obiiter.IBioSequence,
 			j++
 		} else {
 			log.Warnf("Taxid %d is not described in the taxonomy."+
-				      " Sequence %s is discared from the reference database", 
-					  seq.Taxid(), seq.Id())
+				" Sequence %s is discared from the reference database",
+				seq.Taxid(), seq.Id())
 		}
 	}
 
diff --git a/pkg/obiutils/minmax.go b/pkg/obiutils/minmax.go
index fdcc10a..1c48440 100644
--- a/pkg/obiutils/minmax.go
+++ b/pkg/obiutils/minmax.go
@@ -4,20 +4,6 @@ import (
 	"golang.org/x/exp/constraints"
 )
 
-func Min[T constraints.Ordered](x, y T) T {
-	if x < y {
-		return x
-	}
-	return y
-}
-
-func Max[T constraints.Ordered](x, y T) T {
-	if x < y {
-		return y
-	}
-	return x
-}
-
 func MinMax[T constraints.Ordered](x, y T) (T, T) {
 	if x < y {
 		return x, y
@@ -25,7 +11,6 @@ func MinMax[T constraints.Ordered](x, y T) (T, T) {
 	return y, x
 }
 
-
 func MinMaxSlice[T constraints.Ordered](vec []T) (min, max T) {
 	if len(vec) == 0 {
 		panic("empty slice")