Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.

cmd/obitools/obicomplement/main.go

@@ -14,7 +14,7 @@ func main() {
 	optionParser := obioptions.GenerateOptionParser(
 		"obicomplement",
 		"reverse complement of sequences",
-		obiconvert.OptionSet)
+		obiconvert.OptionSet(true))
 
 	_, args := optionParser(os.Args)
 

cmd/obitools/obiconvert/main.go

@@ -17,7 +17,7 @@ func main() {
 	optionParser := obioptions.GenerateOptionParser(
 		"obiconvert",
 		"convertion of sequence files to various formats",
-		obiconvert.OptionSet)
+		obiconvert.OptionSet(true))
 
 	_, args := optionParser(os.Args)
 

pkg/obialign/alignment.go

@@ -169,7 +169,7 @@ func BuildQualityConsensus(seqA, seqB *obiseq.BioSequence, path []int, statOnMis
 
 	right = len(*bufferQA) - right
 
-	// log.Warnf("BuildQualityConsensus: left = %d right = %d\n", left, right)
+	// obilog.Warnf("BuildQualityConsensus: left = %d right = %d\n", left, right)
 
 	for i, qA = range *bufferQA {
 		nA := (*bufferSA)[i]

pkg/obialign/dnamatrix.go

@@ -117,7 +117,7 @@ func _MatchScoreRatio(QF, QR byte) (float64, float64) {
 	term1 := _Logaddexp(qF, qR)
 	term2 := _Logdiffexp(term1, qF+qR)
 
-	// log.Warnf("MatchScoreRatio: %v, %v , %v, %v", QF, QR, term1, term2)
+	// obilog.Warnf("MatchScoreRatio: %v, %v , %v, %v", QF, QR, term1, term2)
 
 	match_logp := _Log1mexp(term2 + l3 - l4)
 	match_score := match_logp - _Log1mexp(match_logp)

pkg/obialign/locatepattern.go

@@ -152,7 +152,7 @@ func LocatePattern(id string, pattern, sequence []byte) (int, int, int) {
 
 	}
 
-	// log.Warnf("from : %d to: %d error: %d match: %v",
+	// obilog.Warnf("from : %d to: %d error: %d match: %v",
 	// 	i, end+1, -buffer[buffIndex(len(sequence)-1, len(pattern)-1, width)],
 	// 	string(sequence[i:(end+1)]))
 	return i, end + 1, -buffer[buffIndex(len(sequence)-1, len(pattern)-1, width)]

pkg/obialign/readalign.go

@@ -53,10 +53,10 @@ func ReadAlign(seqA, seqB *obiseq.BioSequence,
 		over = min(seqA.Len(), seqB.Len())
 	}
 
-	// log.Warnf("fw/fw: %v shift=%d fastCount=%d/over=%d fastScore=%f",
+	// obilog.Warnf("fw/fw: %v shift=%d fastCount=%d/over=%d fastScore=%f",
 	// 	directAlignment, shift, fastCount, over, fastScore)
 
-	// log.Warnf(("seqA: %s\nseqB: %s\n"), seqA.String(), seqB.String())
+	// obilog.Warnf(("seqA: %s\nseqB: %s\n"), seqA.String(), seqB.String())
 
 	// At least one mismatch exists in the overlaping region
 	if fastCount+3 < over {

pkg/obiapat/pattern.go

@@ -410,8 +410,8 @@ func (pattern ApatPattern) FilterBestMatch(sequence ApatSequence, begin, length
 
 	best := [3]int{0, 0, 10000}
 	for _, m := range res {
-		// log.Warnf("Current : Begin : %d End : %d Err : %d", m[0], m[1], m[2])
+		// obilog.Warnf("Current : Begin : %d End : %d Err : %d", m[0], m[1], m[2])
-		// log.Warnf("Best    : Begin : %d End : %d Err : %d", best[0], best[1], best[2])
+		// obilog.Warnf("Best    : Begin : %d End : %d Err : %d", best[0], best[1], best[2])
 		if (m[0] - m[2]) < best[1]+best[2] {
 			// match are overlapping
 			// log.Warnln("overlap")
@@ -467,7 +467,7 @@ func (pattern ApatPattern) AllMatches(sequence ApatSequence, begin, length int)
 		// Recompute the start and end position of the match
 		// when the pattern allows for indels
 		if m[2] > 0 && pattern.pointer.pointer.hasIndel {
-			// log.Warnf("Locating indel on sequence %s[%s]", sequence.pointer.reference.Id(), pattern.String())
+			// obilog.Warnf("Locating indel on sequence %s[%s]", sequence.pointer.reference.Id(), pattern.String())
 			start := m[0] - m[2]*2
 			start = max(start, 0)
 			end := start + int(pattern.pointer.pointer.patlen) + 4*m[2]
@@ -489,7 +489,7 @@ func (pattern ApatPattern) AllMatches(sequence ApatSequence, begin, length int)
 			m[0] = start + pb
 			m[1] = start + pe
 
-			// log.Warnf("seq[%d@%d:%d] %d: %s %d - %s:%s:%s", i, m[0], m[1], olderr, sequence.pointer.reference.Id(), score,
+			// obilog.Warnf("seq[%d@%d:%d] %d: %s %d - %s:%s:%s", i, m[0], m[1], olderr, sequence.pointer.reference.Id(), score,
 			// 	frg, (*cpattern)[0:int(pattern.pointer.pointer.patlen)], sequence.pointer.reference.Sequence()[m[0]:m[1]])
 		}
 

pkg/obidefault/logger.go

@@ -0,0 +1,11 @@
+package obidefault
+
+var __silent_warning__ = false
+
+func SilentWarning() bool {
+	return __silent_warning__
+}
+
+func SilentWarningPtr() *bool {
+	return &__silent_warning__
+}

pkg/obiformats/fastaseq_read.go

@@ -213,7 +213,7 @@ func _ParseFastaFile(
 
 	for chunks := range input {
 		sequences, err := parser(chunks.Source, chunks.Raw)
-		// log.Warnf("Chunck(%d:%d) -%d- ", chunks.Order, l, sequences.Len())
+		// obilog.Warnf("Chunck(%d:%d) -%d- ", chunks.Order, l, sequences.Len())
 
 		if err != nil {
 			log.Fatalf("File %s : Cannot parse the fasta file : %v", chunks.Source, err)

pkg/obiformats/fastqseq_read.go

@@ -17,7 +17,7 @@ import (
 func EndOfLastFastqEntry(buffer []byte) int {
 	var i int
 
-	// log.Warnf("EndOfLastFastqEntry(%d): %s", len(buffer), string(buffer[0:20]))
+	// obilog.Warnf("EndOfLastFastqEntry(%d): %s", len(buffer), string(buffer[0:20]))
 	imax := len(buffer)
 	state := 0
 	restart := imax - 1
@@ -74,7 +74,7 @@ func EndOfLastFastqEntry(buffer []byte) int {
 				state = 3
 			} else {
 				// it was not the sequence part
-				// log.Warnf("it was not the sequence part : %c", C)
+				// obilog.Warnf("it was not the sequence part : %c", C)
 				state = 0
 				i = restart
 			}
@@ -101,7 +101,7 @@ func EndOfLastFastqEntry(buffer []byte) int {
 				// log.Warn("====> End of the last sequence")
 				state = 7
 			} else {
-				// log.Warnf("%s: Strange it was not the end of the last sequence : %c : %s", string(buffer[0:40]), C, string(buffer[i-20:i+5]))
+				// obilog.Warnf("%s: Strange it was not the end of the last sequence : %c : %s", string(buffer[0:40]), C, string(buffer[i-20:i+5]))
 				state = 5
 			}
 		}

pkg/obiformats/fastseq_write_fasta.go

@@ -12,6 +12,7 @@ import (
 	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
@@ -106,7 +107,7 @@ func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader, ski
 			// Handle empty sequences
 			if skipEmpty {
 				// Skip empty sequences if skipEmpty is true
-				log.Warnf("Sequence %s is empty and skipped in output", seq.Id())
+				obilog.Warnf("Sequence %s is empty and skipped in output", seq.Id())
 			} else {
 				// Terminate the program if skipEmpty is false
 				log.Fatalf("Sequence %s is empty", seq.Id())

pkg/obiformats/fastseq_write_fastq.go

@@ -9,6 +9,7 @@ import (
 	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
@@ -75,7 +76,7 @@ func FormatFastqBatch(batch obiiter.BioSequenceBatch,
 
 		} else {
 			if skipEmpty {
-				log.Warnf("Sequence %s is empty and skiped in output", seq.Id())
+				obilog.Warnf("Sequence %s is empty and skiped in output", seq.Id())
 			} else {
 				log.Fatalf("Sequence %s is empty", seq.Id())
 			}

pkg/obiformats/file_chunk_read.go

@@ -172,7 +172,7 @@ func ReadFileChunk(
 				} else {
 					end = -1
 				}
-				// log.Warnf("Splitter not found, attempting %d to read in %d B increments : len(buff) = %d/%d", ic, fileChunkSize, len(extbuff), len(buff))
+				// obilog.Warnf("Splitter not found, attempting %d to read in %d B increments : len(buff) = %d/%d", ic, fileChunkSize, len(extbuff), len(buff))
 			}
 
 			pieces = pieces.Head().Pack()
@@ -204,7 +204,7 @@ func ReadFileChunk(
 				}
 
 				if len(pieces.data) > 0 {
-					// log.Warnf("chuck %d :Read %d bytes from file %s", i, io.Len(), source)
+					// obilog.Warnf("chuck %d :Read %d bytes from file %s", i, io.Len(), source)
 					chunk_channel <- pieces.FileChunk(source, i)
 					i++
 				}

pkg/obiformats/ngsfilter_read.go

@@ -13,6 +13,7 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obingslibrary"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
@@ -663,7 +664,7 @@ func ReadCSVNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
 		if ok {
 			setparam(&ngsfilter, data...)
 		} else {
-			log.Warnf("At line %d: Skipping unknown parameter %s: %v", i, param, data)
+			obilog.Warnf("At line %d: Skipping unknown parameter %s: %v", i, param, data)
 		}
 	}
 

pkg/obifp/uint128.go

@@ -4,6 +4,7 @@ import (
 	"math"
 	"math/bits"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
 	log "github.com/sirupsen/logrus"
 )
 
@@ -46,7 +47,7 @@ func (u Uint128) IsZero() bool {
 // Returns a Uint64 value.
 func (u Uint128) Uint64() Uint64 {
 	if u.w1 != 0 {
-		log.Warnf("Uint128 overflow at Uint64(%v)", u)
+		obilog.Warnf("Uint128 overflow at Uint64(%v)", u)
 	}
 	return Uint64{w0: u.w0}
 }

pkg/obifp/uint256.go

@@ -4,6 +4,7 @@ import (
 	"math"
 	"math/bits"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
 	log "github.com/sirupsen/logrus"
 )
 
@@ -51,7 +52,7 @@ func (u Uint256) IsZero() bool {
 // Returns a Uint64 value.
 func (u Uint256) Uint64() Uint64 {
 	if u.w3 != 0 || u.w2 != 0 || u.w1 != 0 {
-		log.Warnf("Uint256 overflow at Uint64(%v)", u)
+		obilog.Warnf("Uint256 overflow at Uint64(%v)", u)
 	}
 	return Uint64{w0: u.w0}
 }
@@ -64,7 +65,7 @@ func (u Uint256) Uint64() Uint64 {
 // Returns a Uint128 value.
 func (u Uint256) Uint128() Uint128 {
 	if u.w3 != 0 || u.w2 != 0 {
-		log.Warnf("Uint256 overflow at Uint128(%v)", u)
+		obilog.Warnf("Uint256 overflow at Uint128(%v)", u)
 	}
 	return Uint128{u.w1, u.w0}
 }

pkg/obifp/uint64.go

@@ -4,6 +4,7 @@ import (
 	"math"
 	"math/bits"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
 	log "github.com/sirupsen/logrus"
 )
 
@@ -100,7 +101,7 @@ func (u Uint64) LeftShift64(n uint, carryIn uint64) (value, carry uint64) {
 
 	}
 
-	log.Warnf("Uint64 overflow at LeftShift64(%v, %v)", u, n)
+	obilog.Warnf("Uint64 overflow at LeftShift64(%v, %v)", u, n)
 	return 0, 0
 }
 
@@ -129,7 +130,7 @@ func (u Uint64) RightShift64(n uint, carryIn uint64) (value, carry uint64) {
 		return carryIn, u.w0 >> (n - 64)
 	}
 
-	log.Warnf("Uint64 overflow at RightShift64(%v, %v)", u, n)
+	obilog.Warnf("Uint64 overflow at RightShift64(%v, %v)", u, n)
 	return 0, 0
 }
 

pkg/obiiter/limitmemory.go

@@ -3,8 +3,8 @@ package obiiter
 import (
 	"runtime"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
 	"github.com/pbnjay/memory"
-	log "github.com/sirupsen/logrus"
 )
 
 func (iterator IBioSequence) LimitMemory(fraction float64) IBioSequence {
@@ -25,11 +25,11 @@ func (iterator IBioSequence) LimitMemory(fraction float64) IBioSequence {
 				runtime.Gosched()
 				nwait++
 				if nwait%1000 == 0 {
-					log.Warnf("Wait for memory limit %f/%f", fracLoad(), fraction)
+					obilog.Warnf("Wait for memory limit %f/%f", fracLoad(), fraction)
 
 				}
 				if nwait > 10000 {
-					log.Warnf("Very long wait for memory limit %f/%f", fracLoad(), fraction)
+					obilog.Warnf("Very long wait for memory limit %f/%f", fracLoad(), fraction)
 					break
 				}
 			}

pkg/obikmer/kmermap.go

@@ -6,9 +6,9 @@ import (
 	"unsafe"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obifp"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"github.com/schollz/progressbar/v3"
-	log "github.com/sirupsen/logrus"
 )
 
 type KmerMap[T obifp.FPUint[T]] struct {
@@ -226,12 +226,12 @@ func NewKmerMap[T obifp.FPUint[T]](
 	sparseAt := -1
 
 	if sparse && kmersize%2 == 0 {
-		log.Warnf("Kmer size must be odd when using sparse mode")
+		obilog.Warnf("Kmer size must be odd when using sparse mode")
 		kmersize++
 	}
 
 	if !sparse && kmersize%2 == 1 {
-		log.Warnf("Kmer size must be even when not using sparse mode")
+		obilog.Warnf("Kmer size must be even when not using sparse mode")
 		kmersize--
 
 	}

pkg/obilog/warning.go

@@ -0,0 +1,12 @@
+package obilog
+
+import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
+	"github.com/sirupsen/logrus"
+)
+
+func Warnf(format string, args ...interface{}) {
+	if !obidefault.SilentWarning() {
+		logrus.Warnf(format, args...)
+	}
+}

pkg/obilua/lua.go

@@ -8,6 +8,7 @@ import (
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	log "github.com/sirupsen/logrus"
 	lua "github.com/yuin/gopher-lua"
@@ -230,7 +231,7 @@ func LuaProcessor(iterator obiiter.IBioSequence, name, program string, breakOnEr
 				if breakOnError {
 					log.Fatalf("Error during Lua sequence processing : %v", err)
 				} else {
-					log.Warnf("Error during Lua sequence processing : %v", err)
+					obilog.Warnf("Error during Lua sequence processing : %v", err)
 				}
 			}
 

pkg/obingslibrary/multimatch.go

@@ -87,7 +87,7 @@ func lookForTag(seq string, delimiter byte) string {
 
 	i := len(seq) - 1
 
-	// log.Warnf("Provided fragment : %s", string(seq))
+	// obilog.Warnf("Provided fragment : %s", string(seq))
 
 	for i >= 0 && seq[i] != delimiter {
 		i--
@@ -109,7 +109,7 @@ func lookForTag(seq string, delimiter byte) string {
 		return ""
 	}
 
-	// log.Warnf("extracted : %s", string(seq[begin:end]))
+	// obilog.Warnf("extracted : %s", string(seq[begin:end]))
 	return seq[begin:end]
 }
 
@@ -340,8 +340,8 @@ func (marker *Marker) beginTagExtractor(
 	sequence *obiseq.BioSequence,
 	begin int,
 	forward bool) string {
-	// log.Warnf("Forward : %v -> %d %c", forward, marker.Forward_spacer, marker.Forward_tag_delimiter)
+	// obilog.Warnf("Forward : %v -> %d %c", forward, marker.Forward_spacer, marker.Forward_tag_delimiter)
-	// log.Warnf("Forward : %v -> %d %c", forward, marker.Reverse_spacer, marker.Reverse_tag_delimiter)
+	// obilog.Warnf("Forward : %v -> %d %c", forward, marker.Reverse_spacer, marker.Reverse_tag_delimiter)
 	if forward {
 		if marker.Forward_tag_length == 0 {
 			return ""
@@ -351,10 +351,10 @@ func (marker *Marker) beginTagExtractor(
 			return marker.beginFixedTagExtractor(sequence, begin, forward)
 		} else {
 			if marker.Forward_tag_indels == 0 {
-				// log.Warnf("Delimited tag for forward primers %s", marker.forward.String())
+				// obilog.Warnf("Delimited tag for forward primers %s", marker.forward.String())
 				return marker.beginDelimitedTagExtractor(sequence, begin, forward)
 			} else {
-				// log.Warnf("Rescue tag for forward primers %s", marker.forward.String())
+				// obilog.Warnf("Rescue tag for forward primers %s", marker.forward.String())
 				return marker.beginRescueTagExtractor(sequence, begin, forward)
 			}
 		}
@@ -367,10 +367,10 @@ func (marker *Marker) beginTagExtractor(
 			return marker.beginFixedTagExtractor(sequence, begin, forward)
 		} else {
 			if marker.Reverse_tag_indels == 0 {
-				// log.Warnf("Delimited tag for reverse/complement primers %s", marker.creverse.String())
+				// obilog.Warnf("Delimited tag for reverse/complement primers %s", marker.creverse.String())
 				return marker.beginDelimitedTagExtractor(sequence, begin, forward)
 			} else {
-				// log.Warnf("Rescue tag for reverse/complement primers %s", marker.creverse.String())
+				// obilog.Warnf("Rescue tag for reverse/complement primers %s", marker.creverse.String())
 				return marker.beginRescueTagExtractor(sequence, begin, forward)
 			}
 		}
@@ -390,10 +390,10 @@ func (marker *Marker) endTagExtractor(
 			return marker.endFixedTagExtractor(sequence, end, forward)
 		} else {
 			if marker.Reverse_tag_indels == 0 {
-				// log.Warnf("Delimited tag for reverse primers %s", marker.reverse.String())
+				// obilog.Warnf("Delimited tag for reverse primers %s", marker.reverse.String())
 				return marker.endDelimitedTagExtractor(sequence, end, forward)
 			} else {
-				// log.Warnf("Rescue tag for reverse primers %s", marker.reverse.String())
+				// obilog.Warnf("Rescue tag for reverse primers %s", marker.reverse.String())
 				return marker.endRescueTagExtractor(sequence, end, forward)
 			}
 		}
@@ -406,10 +406,10 @@ func (marker *Marker) endTagExtractor(
 			return marker.endFixedTagExtractor(sequence, end, forward)
 		} else {
 			if marker.Forward_tag_indels == 0 {
-				// log.Warnf("Delimited tag for forward/complement primers %s", marker.cforward.String())
+				// obilog.Warnf("Delimited tag for forward/complement primers %s", marker.cforward.String())
 				return marker.endDelimitedTagExtractor(sequence, end, forward)
 			} else {
-				// log.Warnf("Rescue tag for forward/complement primers %s", marker.cforward.String())
+				// obilog.Warnf("Rescue tag for forward/complement primers %s", marker.cforward.String())
 				return marker.endRescueTagExtractor(sequence, end, forward)
 			}
 		}

pkg/obioptions/options.go

@@ -73,6 +73,11 @@ func GenerateOptionParser(program string,
 		options.GetEnv("OBISOLEXA"),
 		options.Description("Decodes quality string according to the Solexa specification."))
 
+	options.BoolVar(obidefault.SilentWarningPtr(), "silent-warning", obidefault.SilentWarning(),
+		options.GetEnv("OBIWARNING"),
+		options.Description("Stop printing of the warning message"),
+	)
+
 	for _, o := range optionset {
 		o(options)
 	}

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 = "8b379d3"
+var _Commit = "2ab6f67"
 var _Version = "Release 4.4.0"
 
 // Version returns the version of the obitools package.

pkg/obiseq/attributes.go

@@ -4,6 +4,7 @@ import (
 	"fmt"
 	"strconv"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	log "github.com/sirupsen/logrus"
 )
@@ -136,7 +137,12 @@ func (s *BioSequence) SetAttribute(key string, value interface{}) {
 	}
 
 	if key == "sequence" {
-		s.SetSequence(value.([]byte))
+		data, err := obiutils.InterfaceToString(value)
+		if err != nil {
+			obilog.Warnf("%s: cannot convert value %v to sequence", s.Id(), value)
+			return
+		}
+		s.SetSequence([]byte(data))
 		return
 	}
 

pkg/obiseq/biosequence.go

@@ -444,6 +444,15 @@ func (s *BioSequence) SetSequence(sequence []byte) {
 	s.sequence = obiutils.InPlaceToLower(CopySlice(sequence))
 }
 
+func (s *BioSequence) HasValidSequence() bool {
+	for _, c := range s.sequence {
+		if !((c >= 'a' && c <= 'z') || c == '-' || c == '.' || c == '[' || c == ']') {
+			return false
+		}
+	}
+	return true
+}
+
 // Setting the qualities of the BioSequence.
 func (s *BioSequence) SetQualities(qualities Quality) {
 	if s.qualities != nil {

pkg/obiseq/biosequenceslice.go

@@ -1,6 +1,7 @@
 package obiseq
 
 import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	log "github.com/sirupsen/logrus"
@@ -61,7 +62,7 @@ func (s *BioSequenceSlice) EnsureCapacity(capacity int) *BioSequenceSlice {
 		if c < capacity {
 			n++
 			if n < 4 {
-				log.Warnf("cannot allocate a Biosequence Slice of size %d (only %d from %d)", capacity, c, old_c)
+				obilog.Warnf("cannot allocate a Biosequence Slice of size %d (only %d from %d)", capacity, c, old_c)
 			} else {
 				log.Panicf("cannot allocate a Biosequence Slice of size %d (only %d from %d)", capacity, c, old_c)
 			}

pkg/obiseq/predicate.go

@@ -5,6 +5,7 @@ import (
 	"fmt"
 	"regexp"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
 	log "github.com/sirupsen/logrus"
 )
 
@@ -278,9 +279,10 @@ func ExpressionPredicat(expression string) SequencePredicate {
 		)
 
 		if err != nil {
-			log.Fatalf("Expression '%s' cannot be evaluated on sequence %s",
+			obilog.Warnf("Expression '%s' cannot be evaluated on sequence %s",
 				expression,
 				sequence.Id())
+			return false
 		}
 
 		return value

pkg/obiseq/taxonomy_methods.go

@@ -6,6 +6,7 @@ import (
 	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
@@ -41,7 +42,7 @@ func (s *BioSequence) SetTaxid(taxid string, rank ...string) {
 			taxon, isAlias, err = taxonomy.Taxon(taxid)
 
 			if err != nil {
-				logger := log.Warnf
+				logger := obilog.Warnf
 				if obidefault.FailOnTaxonomy() {
 					logger = log.Fatalf
 				}
@@ -51,7 +52,7 @@ func (s *BioSequence) SetTaxid(taxid string, rank ...string) {
 
 			if isAlias {
 				if obidefault.UpdateTaxid() {
-					log.Warnf("%s: Taxid: %v is updated to %s",
+					obilog.Warnf("%s: Taxid: %v is updated to %s",
 						s.Id(), taxid, taxon.String())
 					taxid = taxon.String()
 				} else {
@@ -59,7 +60,7 @@ func (s *BioSequence) SetTaxid(taxid string, rank ...string) {
 						log.Fatalf("%s: Taxid: %v is an alias from taxonomy (%v) to %s",
 							s.Id(), taxid, taxonomy.Name(), taxon.String())
 					}
-					log.Warnf("%s: Taxid %v has to be updated to %s",
+					obilog.Warnf("%s: Taxid %v has to be updated to %s",
 						s.Id(), taxid, taxon.String())
 				}
 

pkg/obiseq/taxonomy_predicate.go

@@ -3,6 +3,7 @@ package obiseq
 import (
 	log "github.com/sirupsen/logrus"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
@@ -66,7 +67,7 @@ func IsSubCladeOfSlot(taxonomy *obitax.Taxonomy, key string) SequencePredicate {
 			parent, _, err := taxonomy.Taxon(val)
 
 			if err != nil {
-				log.Warnf("%s: %s is unkown from the taxonomy (%v)", sequence.Id(), val, err)
+				obilog.Warnf("%s: %s is unkown from the taxonomy (%v)", sequence.Id(), val, err)
 			}
 
 			taxon := sequence.Taxon(taxonomy)

pkg/obiseq/worker.go

@@ -4,7 +4,7 @@ import (
 	"fmt"
 	"slices"
 
-	log "github.com/sirupsen/logrus"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
 )
 
 type SeqAnnotator func(*BioSequence)
@@ -119,7 +119,7 @@ func SeqToSliceWorker(worker SeqWorker,
 							s.Id(), err)
 						return BioSequenceSlice{}, err
 					} else {
-						log.Warnf("got an error on sequence %s processing : %v",
+						obilog.Warnf("got an error on sequence %s processing : %v",
 							s.Id(), err)
 					}
 				}
@@ -208,7 +208,7 @@ func SeqToSliceConditionalWorker(
 							s.Id(), err)
 						return BioSequenceSlice{}, err
 					} else {
-						log.Warnf("got an error on sequence %s processing : %v",
+						obilog.Warnf("got an error on sequence %s processing : %v",
 							s.Id(), err)
 					}
 				}

pkg/obistats/kmeans.go

@@ -8,6 +8,7 @@ import (
 	"golang.org/x/exp/rand"
 	"gonum.org/v1/gonum/stat/sampleuv"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	log "github.com/sirupsen/logrus"
 )
@@ -280,7 +281,7 @@ func (clustering *KmeansClustering) AssignToClass() {
 	nreset := clustering.ResetEmptyCenters()
 
 	if nreset > 0 {
-		log.Warnf("Reseted %d empty centers", nreset)
+		obilog.Warnf("Reseted %d empty centers", nreset)
 	}
 }
 

pkg/obitax/taxid.go

@@ -35,7 +35,7 @@ func (f *TaxidFactory) FromString(taxid string) (Taxid, error) {
 	if len(part2) == 0 {
 		taxid = part1
 	} else {
-		//log.Warnf("TaxidFactory.FromString: taxid %s -> -%s- -%s- ", taxid, part1, part2)
+		//obilog.Warnf("TaxidFactory.FromString: taxid %s -> -%s- -%s- ", taxid, part1, part2)
 		if part1 != f.code {
 			return nil, fmt.Errorf("taxid %s string does not start with taxonomy code %s", taxid, f.code)
 		}

pkg/obitools/obiannotate/obiannotate.go

@@ -322,7 +322,7 @@ func CLIAnnotationWorker() obiseq.SeqWorker {
 
 	if CLIHasCut() {
 		from, to := CLICut()
-		w := CutSequenceWorker(from, to, false)
+		w := CutSequenceWorker(from, to, true)
 
 		annotator = annotator.ChainWorkers(w)
 	}

pkg/obitools/obiannotate/options.go

@@ -130,7 +130,7 @@ func SequenceAnnotationOptionSet(options *getoptions.GetOpt) {
 // OptionSet adds to the basic option set every options declared for
 // the obipcr command
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	obigrep.SequenceSelectionOptionSet(options)
 	SequenceAnnotationOptionSet(options)
 }

pkg/obitools/obiclean/chimera.go

@@ -53,7 +53,7 @@ func commonSuffix(a, b *obiseq.BioSequence) int {
 	if obiutils.UnsafeString(as[i+1:]) != obiutils.UnsafeString(bs[j+1:]) {
 		log.Fatalf("i: %d, j: %d (%s/%s)", i, j, as[i+1:], bs[j+1:])
 	}
-	// log.Warnf("i: %d, j: %d (%s)", i, j, as[i+1:])
+	// obilog.Warnf("i: %d, j: %d (%s)", i, j, as[i+1:])
 
 	return l
 }

pkg/obitools/obicleandb/obicleandb.go

@@ -113,10 +113,10 @@ func MakeSequenceFamilyGenusWorker(references obiseq.BioSequenceSlice) obiseq.Se
 			}
 
 			// level, _ := sequence.GetAttribute("obicleandb_level")
-			// log.Warnf("%s - level: %v", sequence.Id(), level)
+			// obilog.Warnf("%s - level: %v", sequence.Id(), level)
-			// log.Warnf("%s - gdist: %v", sequence.Id(), indist)
+			// obilog.Warnf("%s - gdist: %v", sequence.Id(), indist)
-			// log.Warnf("%s - fdist: %v", sequence.Id(), outdist)
+			// obilog.Warnf("%s - fdist: %v", sequence.Id(), outdist)
-			// log.Warnf("%s - pval: %f", sequence.Id(), pval)
+			// obilog.Warnf("%s - pval: %f", sequence.Id(), pval)
 		}
 
 		if pval < 0.0 {

pkg/obitools/obiconvert/options.go

@@ -126,11 +126,16 @@ func PairedFilesOptionSet(options *getoptions.GetOpt) {
 	)
 }
 
-func OptionSet(options *getoptions.GetOpt) {
+func OptionSet(allow_paired bool) func(options *getoptions.GetOpt) {
-	obioptions.LoadTaxonomyOptionSet(options, false, false)
+	f := func(options *getoptions.GetOpt) {
-	InputOptionSet(options)
+		obioptions.LoadTaxonomyOptionSet(options, false, false)
-	OutputOptionSet(options)
+		InputOptionSet(options)
-	PairedFilesOptionSet(options)
+		OutputOptionSet(options)
+		if allow_paired {
+			PairedFilesOptionSet(options)
+		}
+	}
+	return f
 }
 
 // Returns true if the number of reads described in the

pkg/obitools/obidemerge/options.go

@@ -17,7 +17,7 @@ func DemergeOptionSet(options *getoptions.GetOpt) {
 // OptionSet adds to the basic option set every options declared for
 // the obipcr command
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	DemergeOptionSet(options)
 }
 

pkg/obitools/obigrep/options.go

@@ -166,7 +166,7 @@ func SequenceSelectionOptionSet(options *getoptions.GetOpt) {
 // OptionSet adds to the basic option set every options declared for
 // the obipcr command
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(true)(options)
 	SequenceSelectionOptionSet(options)
 
 	options.StringVar(&_SaveRejected, "save-discarded", _SaveRejected,

pkg/obitools/obijoin/options.go

@@ -46,7 +46,7 @@ func JoinOptionSet(options *getoptions.GetOpt) {
 // OptionSet adds to the basic option set every options declared for
 // the obipcr command
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	JoinOptionSet(options)
 }
 

pkg/obitools/obikmersim/options.go

@@ -76,12 +76,12 @@ func KmerSimMatchOptionSet(options *getoptions.GetOpt) {
 }
 
 func CountOptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	KmerSimCountOptionSet(options)
 }
 
 func MatchOptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	KmerSimCountOptionSet(options)
 	KmerSimMatchOptionSet(options)
 }

pkg/obitools/obimicrosat/options.go

@@ -49,7 +49,7 @@ func MicroSatelliteOptionSet(options *getoptions.GetOpt) {
 }
 
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	MicroSatelliteOptionSet(options)
 }
 

pkg/obitools/obimultiplex/options.go

@@ -54,7 +54,7 @@ func MultiplexOptionSet(options *getoptions.GetOpt) {
 }
 
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	MultiplexOptionSet(options)
 }
 

pkg/obitools/obipcr/options.go

@@ -67,7 +67,7 @@ func PCROptionSet(options *getoptions.GetOpt) {
 // OptionSet adds to the basic option set every options declared for
 // the obipcr command
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	PCROptionSet(options)
 }
 

pkg/obitools/obirefidx/obirefidx.go

@@ -88,7 +88,7 @@ func IndexSequence(seqidx int,
 	// Initialize a matrix to store alignment scores
 	var matrix []uint64
 
-	// log.Warnf("%s : %s", sequence.Id(), pseq.String())
+	// obilog.Warnf("%s : %s", sequence.Id(), pseq.String())
 	for idx_path := 1; idx_path < path_len; idx_path++ {
 		mini := -1
 		seqidcs := refs[pseq.Taxon(idx_path).Node]
@@ -144,8 +144,8 @@ func IndexSequence(seqidx int,
 				}
 
 				if mini == 0 {
-					// log.Warnf("%s: %s", sequence.Id(), sequence.String())
+					// obilog.Warnf("%s: %s", sequence.Id(), sequence.String())
-					// log.Warnf("%s: %s", suject.Id(), suject.String())
+					// obilog.Warnf("%s: %s", suject.Id(), suject.String())
 					break
 				}
 			}
@@ -158,7 +158,7 @@ func IndexSequence(seqidx int,
 			// insure than closest is strictly increasing
 			for k := idx_path - 1; k >= 0 && mini < closest[k]; k-- {
 				closest[k] = mini
-				// log.Warnf("(%s,%s) Smaller alignment found than previous (%d,%d). Resetting closest.", sequence.Id(), pseq.Taxon(idx_path).String(), mini, closest[k])
+				// obilog.Warnf("(%s,%s) Smaller alignment found than previous (%d,%d). Resetting closest.", sequence.Id(), pseq.Taxon(idx_path).String(), mini, closest[k])
 			}
 		} else {
 			closest[idx_path] = seq_len
@@ -167,7 +167,7 @@ func IndexSequence(seqidx int,
 
 	obitag_index := make(map[int]string, pseq.Len())
 
-	// log.Warnf("(%s,%s): %v", sequence.Id(), pseq.Taxon(0).String(), closest)
+	// obilog.Warnf("(%s,%s): %v", sequence.Id(), pseq.Taxon(0).String(), closest)
 	for i, d := range closest {
 		if i < (len(closest)-1) && d < closest[i+1] {
 			current_taxon := pseq.Taxon(i)

pkg/obitools/obirefidx/options.go

@@ -8,5 +8,5 @@ import (
 // OptionSet adds to the basic option set every options declared for
 // the obiuniq command
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 }

pkg/obitools/obiscript/options.go

@@ -26,7 +26,7 @@ func ScriptOptionSet(options *getoptions.GetOpt) {
 
 func OptionSet(options *getoptions.GetOpt) {
 	ScriptOptionSet(options)
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	obigrep.SequenceSelectionOptionSet(options)
 }
 

pkg/obitools/obisplit/options.go

@@ -39,7 +39,7 @@ func SplitOptionSet(options *getoptions.GetOpt) {
 
 func OptionSet(options *getoptions.GetOpt) {
 	SplitOptionSet(options)
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 }
 
 func CLIHasConfig() bool {

pkg/obitools/obitag/obitag.go

@@ -11,6 +11,7 @@ import (
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obikmer"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obirefidx"
@@ -260,7 +261,7 @@ func CLIAssignTaxonomy(iterator obiiter.IBioSequence,
 		if taxon != nil {
 			j++
 		} else {
-			log.Warnf("Taxid %s is not described in the taxonomy %s."+
+			obilog.Warnf("Taxid %s is not described in the taxonomy %s."+
 				" Sequence %s is discared from the reference database",
 				seq.Taxid(), taxo.Name(), seq.Id())
 		}

pkg/obitools/obitag/options.go

@@ -41,7 +41,7 @@ func TagOptionSet(options *getoptions.GetOpt) {
 // OptionSet adds to the basic option set every options declared for
 // the obiuniq command
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	TagOptionSet(options)
 }
 

pkg/obitools/obiuniq/options.go

@@ -45,13 +45,12 @@ func UniqueOptionSet(options *getoptions.GetOpt) {
 
 }
 
-
 // OptionSet adds to the basic option set every options declared for
 // the obiuniq command
 //
 // It takes a pointer to a GetOpt struct as its parameter and does not return anything.
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	UniqueOptionSet(options)
 }
 
@@ -150,4 +149,4 @@ func CLINoSingleton() bool {
 // noSingleton bool - The boolean value to set for _NoSingleton.
 func SetNoSingleton(noSingleton bool) {
 	_NoSingleton = noSingleton
-}
+}