Produce less weird crash on non existing files

Former-commit-id: 74bb27bd53c685be530632994bd2ba24c1f362e1

cmd/obitools/obiannotate/main.go

@@ -2,6 +2,7 @@ package main
 
 import (
 	"os"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
@@ -34,7 +35,13 @@ func main() {
 
 	_, args := optionParser(os.Args)
 
-	sequences, _ := obiconvert.CLIReadBioSequences(args...)
+	sequences, err := obiconvert.CLIReadBioSequences(args...)
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)",err)
+		os.Exit(1)
+	}
+
 	annotator := obiannotate.CLIAnnotationPipeline()
 	obiconvert.CLIWriteBioSequences(sequences.Pipe(annotator), true)
 

cmd/obitools/obiclean/main.go

@@ -2,6 +2,7 @@ package main
 
 import (
 	"os"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiclean"
@@ -15,7 +16,12 @@ func main() {
 
 	_, args := optionParser(os.Args)
 
-	fs, _ := obiconvert.CLIReadBioSequences(args...)
+	fs, err := obiconvert.CLIReadBioSequences(args...)
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)",err)
+		os.Exit(1)
+	}
 
 	cleaned := obiclean.IOBIClean(fs)
 

cmd/obitools/obicleandb/main.go

@@ -2,6 +2,7 @@ package main
 
 import (
 	"os"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obicleandb"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
@@ -14,7 +15,12 @@ func main() {
 
 	_, args := optionParser(os.Args)
 
-	fs, _ := obiconvert.CLIReadBioSequences(args...)
+	fs, err := obiconvert.CLIReadBioSequences(args...)
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)",err)
+		os.Exit(1)
+	}
 
 	cleaned := obicleandb.ICleanDB(fs)
 

cmd/obitools/obicomplement/main.go

@@ -2,6 +2,7 @@ package main
 
 import (
 	"os"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
@@ -15,7 +16,12 @@ func main() {
 
 	_, args := optionParser(os.Args)
 
-	fs, _ := obiconvert.CLIReadBioSequences(args...)
+	fs, err := obiconvert.CLIReadBioSequences(args...)
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)",err)
+		os.Exit(1)
+	}
 
 	comp := fs.MakeIWorker(obiseq.ReverseComplementWorker(true))
 	obiconvert.CLIWriteBioSequences(comp, true)

cmd/obitools/obiconvert/main.go

@@ -2,6 +2,7 @@ package main
 
 import (
 	"os"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
@@ -14,7 +15,13 @@ func main() {
 
 	_, args := optionParser(os.Args)
 
-	fs, _ := obiconvert.CLIReadBioSequences(args...)
+	fs, err := obiconvert.CLIReadBioSequences(args...)
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)",err)
+		os.Exit(1)
+	}
+
 	obiconvert.CLIWriteBioSequences(fs, true)
 
 	obiiter.WaitForLastPipe()

cmd/obitools/obicount/main.go

@@ -3,6 +3,7 @@ package main
 import (
 	"fmt"
 	"os"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obicount"
@@ -33,7 +34,13 @@ func main() {
 
 	_, args := optionParser(os.Args)
 
-	fs, _ := obiconvert.CLIReadBioSequences(args...)
+	fs, err := obiconvert.CLIReadBioSequences(args...)
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)",err)
+		os.Exit(1)
+	}
+
 	nvariant, nread, nsymbol := fs.Count(true)
 
 	if obicount.CLIIsPrintingVariantCount() {

cmd/obitools/obicsv/main.go

@@ -2,6 +2,7 @@ package main
 
 import (
 	"os"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
@@ -14,7 +15,13 @@ func main() {
 
 	_, args := optionParser(os.Args)
 
-	fs, _ := obiconvert.CLIReadBioSequences(args...)
+	fs, err := obiconvert.CLIReadBioSequences(args...)
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)",err)
+		os.Exit(1)
+	}
+
 	obicsv.CLIWriteCSV(fs, true)
 
 	obiiter.WaitForLastPipe()

cmd/obitools/obidistribute/main.go

@@ -2,6 +2,7 @@ package main
 
 import (
 	"os"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
@@ -15,7 +16,12 @@ func main() {
 
 	_, args := optionParser(os.Args)
 
-	fs, _ := obiconvert.CLIReadBioSequences(args...)
+	fs, err := obiconvert.CLIReadBioSequences(args...)
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)",err)
+		os.Exit(1)
+	}
 
 	obidistribute.DistributeSequence(fs)
 

cmd/obitools/obigrep/main.go

@@ -2,6 +2,7 @@ package main
 
 import (
 	"os"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
@@ -34,7 +35,12 @@ func main() {
 
 	_, args := optionParser(os.Args)
 
-	sequences, _ := obiconvert.CLIReadBioSequences(args...)
+	sequences, err := obiconvert.CLIReadBioSequences(args...)
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)",err)
+		os.Exit(1)
+	}
 	selected := obigrep.CLIFilterSequence(sequences)
 	obiconvert.CLIWriteBioSequences(selected, true)
 	obiiter.WaitForLastPipe()

cmd/obitools/obimultiplex/main.go

@@ -2,6 +2,7 @@ package main
 
 import (
 	"os"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
@@ -29,7 +30,12 @@ func main() {
 
 	_, args := optionParser(os.Args)
 
-	sequences, _ := obiconvert.CLIReadBioSequences(args...)
+	sequences, err := obiconvert.CLIReadBioSequences(args...)
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)",err)
+		os.Exit(1)
+	}
 	amplicons, _ := obimultiplex.IExtractBarcode(sequences)
 	obiconvert.CLIWriteBioSequences(amplicons, true)
 	amplicons.Wait()

cmd/obitools/obipairing/main.go

@@ -2,6 +2,7 @@ package main
 
 import (
 	"os"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
@@ -30,7 +31,13 @@ func main() {
 	optionParser := obioptions.GenerateOptionParser(obipairing.OptionSet)
 
 	optionParser(os.Args)
-	pairs, _ := obipairing.CLIPairedSequence()
+	pairs, err := obipairing.CLIPairedSequence()
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)",err)
+		os.Exit(1)
+	}
+
 	paired := obipairing.IAssemblePESequencesBatch(pairs,
 		obipairing.CLIGapPenality(),
 		obipairing.CLIDelta(),

cmd/obitools/obipcr/main.go

@@ -2,6 +2,7 @@ package main
 
 import (
 	"os"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
@@ -31,7 +32,13 @@ func main() {
 
 	_, args := optionParser(os.Args)
 
-	sequences, _ := obiconvert.CLIReadBioSequences(args...)
+	sequences, err := obiconvert.CLIReadBioSequences(args...)
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)",err)
+		os.Exit(1)
+	}
+
 	amplicons, _ := obipcr.PCR(sequences)
 	obiconvert.CLIWriteBioSequences(amplicons, true)
 	obiiter.WaitForLastPipe()

cmd/obitools/obirefidx/main.go

@@ -2,6 +2,7 @@ package main
 
 import (
 	"os"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
@@ -15,7 +16,12 @@ func main() {
 
 	_, args := optionParser(os.Args)
 
-	fs, _ := obiconvert.CLIReadBioSequences(args...)
+	fs, err := obiconvert.CLIReadBioSequences(args...)
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)",err)
+		os.Exit(1)
+	}
 	indexed := obirefidx.IndexReferenceDB(fs)
 
 	obiconvert.CLIWriteBioSequences(indexed, true)

cmd/obitools/obitag/main.go

@@ -3,6 +3,7 @@ package main
 import (
 	"fmt"
 	"os"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
@@ -33,7 +34,13 @@ func main() {
 
 	_, args := optionParser(os.Args)
 
-	fs, _ := obiconvert.CLIReadBioSequences(args...)
+	fs, err := obiconvert.CLIReadBioSequences(args...)
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)",err)
+		os.Exit(1)
+	}
+
 	identified := obitag.AssignTaxonomy(fs)
 
 	obiconvert.CLIWriteBioSequences(identified, true)

cmd/obitools/obiuniq/main.go

@@ -2,6 +2,7 @@ package main
 
 import (
 	"os"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
@@ -34,7 +35,13 @@ func main() {
 
 	_, args := optionParser(os.Args)
 
-	sequences, _ := obiconvert.CLIReadBioSequences(args...)
+	sequences, err := obiconvert.CLIReadBioSequences(args...)
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)",err)
+		os.Exit(1)
+	}
+
 	unique := obiuniq.Unique(sequences)
 	obiconvert.CLIWriteBioSequences(unique, true)
 

go.mod

@@ -11,7 +11,7 @@ require (
 	github.com/klauspost/pgzip v1.2.5
 	github.com/rrethy/ahocorasick v1.0.0
 	github.com/schollz/progressbar/v3 v3.8.6
-	github.com/sirupsen/logrus v1.8.1
+	github.com/sirupsen/logrus v1.9.0
 	github.com/tevino/abool/v2 v2.0.1
 	gonum.org/v1/gonum v0.11.0
 	scientificgo.org/special v0.0.0
@@ -23,7 +23,7 @@ require (
 	github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db // indirect
 	github.com/rivo/uniseg v0.2.0 // indirect
 	golang.org/x/crypto v0.0.0-20220131195533-30dcbda58838 // indirect
-	golang.org/x/exp v0.0.0-20191002040644-a1355ae1e2c3 // indirect
+	golang.org/x/exp v0.0.0-20230306221820-f0f767cdffd6 // indirect
-	golang.org/x/sys v0.0.0-20220722155257-8c9f86f7a55f // indirect
+	golang.org/x/sys v0.1.0 // indirect
 	golang.org/x/term v0.0.0-20210927222741-03fcf44c2211 // indirect
 )

go.sum

@@ -37,10 +37,14 @@ github.com/schollz/progressbar/v3 v3.8.6 h1:QruMUdzZ1TbEP++S1m73OqRJk20ON11m6Wqv
 github.com/schollz/progressbar/v3 v3.8.6/go.mod h1:W5IEwbJecncFGBvuEh4A7HT1nZZ6WNIL2i3qbnI0WKY=
 github.com/sirupsen/logrus v1.8.1 h1:dJKuHgqk1NNQlqoA6BTlM1Wf9DOH3NBjQyu0h9+AZZE=
 github.com/sirupsen/logrus v1.8.1/go.mod h1:yWOB1SBYBC5VeMP7gHvWumXLIWorT60ONWic61uBYv0=
+github.com/sirupsen/logrus v1.9.0 h1:trlNQbNUG3OdDrDil03MCb1H2o9nJ1x4/5LYw7byDE0=
+github.com/sirupsen/logrus v1.9.0/go.mod h1:naHLuLoDiP4jHNo9R0sCBMtWGeIprob74mVsIT4qYEQ=
 github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
 github.com/stretchr/testify v1.2.2/go.mod h1:a8OnRcib4nhh0OaRAV+Yts87kKdq0PP7pXfy6kDkUVs=
 github.com/stretchr/testify v1.3.0 h1:TivCn/peBQ7UY8ooIcPgZFpTNSz0Q2U6UrFlUfqbe0Q=
 github.com/stretchr/testify v1.3.0/go.mod h1:M5WIy9Dh21IEIfnGCwXGc5bZfKNJtfHm1UVUgZn+9EI=
+github.com/stretchr/testify v1.7.0 h1:nwc3DEeHmmLAfoZucVR881uASk0Mfjw8xYJ99tb5CcY=
+github.com/stretchr/testify v1.7.0/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg=
 github.com/tevino/abool/v2 v2.0.1 h1:OF7FC5V5z3yAWyixbc32ecEzrgAJCsPkVOsPM2qoZPI=
 github.com/tevino/abool/v2 v2.0.1/go.mod h1:+Lmlqk6bHDWHqN1cbxqhwEAwMPXgc8I1SDEamtseuXY=
 golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w=
@@ -50,6 +54,8 @@ golang.org/x/crypto v0.0.0-20220131195533-30dcbda58838/go.mod h1:IxCIyHEi3zRg3s0
 golang.org/x/exp v0.0.0-20190306152737-a1d7652674e8/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA=
 golang.org/x/exp v0.0.0-20191002040644-a1355ae1e2c3 h1:n9HxLrNxWWtEb1cA950nuEEj3QnKbtsCJ6KjcgisNUs=
 golang.org/x/exp v0.0.0-20191002040644-a1355ae1e2c3/go.mod h1:NOZ3BPKG0ec/BKJQgnvsSFpcKLM5xXVWnvZS97DWHgE=
+golang.org/x/exp v0.0.0-20230306221820-f0f767cdffd6 h1:3p+wVC0x0TCIPgd3LCQlpgVlEtjziEC5v42w7+B8t8M=
+golang.org/x/exp v0.0.0-20230306221820-f0f767cdffd6/go.mod h1:CxIveKay+FTh1D0yPZemJVgC/95VzuuOLq5Qi4xnoYc=
 golang.org/x/image v0.0.0-20190227222117-0694c2d4d067/go.mod h1:kZ7UVZpmo3dzQBMxlp+ypCbDeSB+sBbTgSJuh5dn5js=
 golang.org/x/image v0.0.0-20190802002840-cff245a6509b/go.mod h1:FeLwcggjj3mMvU+oOTbSwawSJRM1uh48EjtB4UJZlP0=
 golang.org/x/mobile v0.0.0-20190719004257-d2bd2a29d028/go.mod h1:E/iHnbuqvinMTCcRqshq8CkpyQDoeVncDDYHnLhea+o=
@@ -67,8 +73,11 @@ golang.org/x/sys v0.0.0-20210423082822-04245dca01da/go.mod h1:h1NjWce9XRLGQEsW7w
 golang.org/x/sys v0.0.0-20210615035016-665e8c7367d1/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
 golang.org/x/sys v0.0.0-20210630005230-0f9fa26af87c/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
 golang.org/x/sys v0.0.0-20220128215802-99c3d69c2c27/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
+golang.org/x/sys v0.0.0-20220715151400-c0bba94af5f8/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
 golang.org/x/sys v0.0.0-20220722155257-8c9f86f7a55f h1:v4INt8xihDGvnrfjMDVXGxw9wrfxYyCjk0KbXjhR55s=
 golang.org/x/sys v0.0.0-20220722155257-8c9f86f7a55f/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
+golang.org/x/sys v0.1.0 h1:kunALQeHf1/185U1i0GOB/fy1IPRDDpuoOOqRReG57U=
+golang.org/x/sys v0.1.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
 golang.org/x/term v0.0.0-20201126162022-7de9c90e9dd1/go.mod h1:bj7SfCRtBDWHUb9snDiAeCFNEtKQo2Wmx5Cou7ajbmo=
 golang.org/x/term v0.0.0-20210927222741-03fcf44c2211 h1:JGgROgKl9N8DuW20oFS5gxc+lE67/N3FcwmBPMe7ArY=
 golang.org/x/term v0.0.0-20210927222741-03fcf44c2211/go.mod h1:jbD1KX2456YbFQfuXm/mYQcufACuNUgVhRMnK/tPxf8=
@@ -79,6 +88,8 @@ golang.org/x/tools v0.0.0-20190927191325-030b2cf1153e/go.mod h1:b+2E5dAYhXwXZwtn
 golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
 gonum.org/v1/gonum v0.11.0 h1:f1IJhK4Km5tBJmaiJXtk/PkL4cdVX6J+tGiM187uT5E=
 gonum.org/v1/gonum v0.11.0/go.mod h1:fSG4YDCxxUZQJ7rKsQrj0gMOg00Il0Z96/qMA4bVQhA=
+gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
+gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
 scientificgo.org/special v0.0.0 h1:P6WJkECo6tgtvZAEfNXl+KEB9ReAatjKAeX8U07mjSc=
 scientificgo.org/special v0.0.0/go.mod h1:LoGVh9tS431RLTJo7gFlYDKFWq44cEb7QqL+M0EKtZU=
 scientificgo.org/testutil v0.0.0 h1:y356DHRo0tAz9zIFmxlhZoKDlHPHaWW/DCm9k3PhIMA=

pkg/obiformats/genbank_read.go

@@ -47,7 +47,7 @@ func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequence) {
 			nl++
 			line := scanner.Text()
 			switch {
-			case state==inDefinition && ! strings.HasPrefix(line, "            "):
+			case state == inDefinition && !strings.HasPrefix(line, "            "):
 				state = inEntry
 				fallthrough
 			case strings.HasPrefix(line, "LOCUS       "):
@@ -61,7 +61,7 @@ func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequence) {
 			case strings.HasPrefix(line, "FEATURES    "):
 				featBytes.WriteString(line)
 				state = inFeature
-			case strings.HasPrefix(line, "ORIGIN      "):
+			case strings.HasPrefix(line, "ORIGIN"):
 				state = inSequence
 			case line == "//":
 				log.Debugln("Total lines := ", nl)
@@ -76,12 +76,15 @@ func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequence) {
 				annot["scientific_name"] = scientificName
 				annot["taxid"] = taxid
 				// log.Println(FormatFasta(sequence, FormatFastSeqJsonHeader))
+				log.Debugf("Read sequences %s: %dbp (%d)", sequence.Id(),
+					sequence.Len(), seqBytes.Len())
+
 				sequences = append(sequences, sequence)
 				defBytes = new(bytes.Buffer)
 				featBytes = new(bytes.Buffer)
 				seqBytes = new(bytes.Buffer)
-				nl=0
+				nl = 0
-				sl=0
+				sl = 0
 			default:
 				switch state {
 				case inDefinition:

pkg/obiformats/universal_read.go

@@ -85,8 +85,8 @@ func ReadSequencesFromFile(filename string,
 	switch filetype {
 	case "fastq", "fasta":
 		file.Close()
-		is, _ := ReadFastSeqFromFile(filename, options...)
+		is, err := ReadFastSeqFromFile(filename, options...)
-		return is, nil
+		return is, err
 	case "ecopcr":
 		return ReadEcoPCR(reader, options...), nil
 	case "embl":

pkg/obiseq/class.go

@@ -90,7 +90,7 @@ func AnnotationClassifier(key string, na string) *BioSequenceClassifier {
 		return AnnotationClassifier(key, na)
 	}
 
-	c := BioSequenceClassifier{code, value, reset, clone,"AnnotationClassifier"}
+	c := BioSequenceClassifier{code, value, reset, clone, "AnnotationClassifier"}
 	return &c
 }
 
@@ -127,7 +127,7 @@ func DualAnnotationClassifier(key1, key2 string, na string) *BioSequenceClassifi
 						val2 = fmt.Sprint(value)
 					}
 				} else {
-					val2=na
+					val2 = na
 				}
 			}
 		}
@@ -173,7 +173,7 @@ func DualAnnotationClassifier(key1, key2 string, na string) *BioSequenceClassifi
 		return DualAnnotationClassifier(key1, key2, na)
 	}
 
-	c := BioSequenceClassifier{code, value, reset, clone,"DualAnnotationClassifier"}
+	c := BioSequenceClassifier{code, value, reset, clone, "DualAnnotationClassifier"}
 	return &c
 }
 
@@ -206,7 +206,7 @@ func PredicateClassifier(predicate SequencePredicate) *BioSequenceClassifier {
 		return PredicateClassifier(predicate)
 	}
 
-	c := BioSequenceClassifier{code, value, reset, clone,"PredicateClassifier"}
+	c := BioSequenceClassifier{code, value, reset, clone, "PredicateClassifier"}
 	return &c
 }
 
@@ -228,7 +228,7 @@ func HashClassifier(size int) *BioSequenceClassifier {
 		return HashClassifier(size)
 	}
 
-	c := BioSequenceClassifier{code, value, reset, clone,"HashClassifier"}
+	c := BioSequenceClassifier{code, value, reset, clone, "HashClassifier"}
 	return &c
 }
 
@@ -283,7 +283,7 @@ func SequenceClassifier() *BioSequenceClassifier {
 		return SequenceClassifier()
 	}
 
-	c := BioSequenceClassifier{code, value, reset, clone,"SequenceClassifier"}
+	c := BioSequenceClassifier{code, value, reset, clone, "SequenceClassifier"}
 	return &c
 }
 
@@ -313,7 +313,6 @@ func RotateClassifier(size int) *BioSequenceClassifier {
 		return RotateClassifier(size)
 	}
 
-	c := BioSequenceClassifier{code, value, reset, clone,"RotateClassifier"}
+	c := BioSequenceClassifier{code, value, reset, clone, "RotateClassifier"}
 	return &c
 }
-

pkg/obitools/obiconvert/sequence_reader.go

@@ -1,6 +1,7 @@
 package obiconvert
 
 import (
+	"fmt"
 	"os"
 	"path/filepath"
 	"strings"
@@ -20,6 +21,9 @@ func _ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
 		err = filepath.Walk(fn,
 			func(path string, info os.FileInfo, err error) error {
 				var e error
+				if info == nil {
+					return fmt.Errorf("cannot open path")
+				}
 				for info.Mode()&os.ModeSymlink == os.ModeSymlink {
 					path, e = filepath.EvalSymlinks(path)
 					if e != nil {