Plenty of small bugs

Former-commit-id: 42c7fab7d65906c80ab4cd32da6867ff21842ea8

pkg/obitools/obimultiplex/options.go

@@ -77,7 +77,7 @@ func CLIHasNGSFilterFile() bool {
 	return _NGSFilterFile != ""
 }
 
-func CLINGSFIlter() (obingslibrary.NGSLibrary, error) {
+func CLINGSFIlter() (*obingslibrary.NGSLibrary, error) {
 	file, err := os.Open(_NGSFilterFile)
 
 	if err != nil {

pkg/obitools/obimultiplex2/demultiplex.go

@@ -0,0 +1,60 @@
+package obimultiplex2
+
+import (
+	log "github.com/sirupsen/logrus"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obingslibrary"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
+)
+
+func IExtractBarcode(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error) {
+
+	opts := make([]obingslibrary.WithOption, 0, 10)
+
+	opts = append(opts,
+		obingslibrary.OptionAllowedMismatches(CLIAllowedMismatch()),
+		obingslibrary.OptionAllowedIndel(CLIAllowsIndel()),
+		obingslibrary.OptionUnidentified(CLIUnidentifiedFileName()),
+		obingslibrary.OptionDiscardErrors(!CLIConservedErrors()),
+		obingslibrary.OptionParallelWorkers(obioptions.CLIParallelWorkers()),
+		obingslibrary.OptionBatchSize(obioptions.CLIBatchSize()),
+	)
+
+	ngsfilter, err := CLINGSFIlter()
+	if err != nil {
+		log.Fatalf("%v", err)
+	}
+
+	worker := ngsfilter.ExtractMultiBarcodeSliceWorker(opts...)
+
+	newIter := iterator.MakeISliceWorker(worker, false)
+
+	if !CLIConservedErrors() {
+		log.Infoln("Discards unassigned sequences")
+		newIter = newIter.FilterOn(obiseq.HasAttribute("demultiplex_error").Not(), obioptions.CLIBatchSize())
+	}
+
+	var unidentified obiiter.IBioSequence
+	if CLIUnidentifiedFileName() != "" {
+		log.Printf("Unassigned sequences saved in file: %s\n", CLIUnidentifiedFileName())
+		unidentified, newIter = newIter.DivideOn(obiseq.HasAttribute("demultiplex_error"),
+			obioptions.CLIBatchSize())
+
+		go func() {
+			_, err := obiconvert.CLIWriteBioSequences(unidentified,
+				true,
+				CLIUnidentifiedFileName())
+
+			if err != nil {
+				log.Fatalf("%v", err)
+			}
+		}()
+
+	}
+	log.Printf("Sequence demultiplexing using %d workers\n", obioptions.CLIParallelWorkers())
+
+	return newIter, nil
+}

pkg/obitools/obimultiplex2/options.go

@@ -0,0 +1,108 @@
+package obimultiplex2
+
+import (
+	"fmt"
+	"os"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obingslibrary"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
+	"github.com/DavidGamba/go-getoptions"
+
+	log "github.com/sirupsen/logrus"
+)
+
+var _NGSFilterFile = ""
+var _askTemplate = false
+var _UnidentifiedFile = ""
+var _AllowedMismatch = int(2)
+var _AllowsIndel = false
+var _ConservedError = false
+
+// PCROptionSet defines every options related to a simulated PCR.
+//
+// The function adds to a CLI every options proposed to the user
+// to tune the parametters of the PCR simulation algorithm.
+//
+// # Parameters
+//
+// - option : is a pointer to a getoptions.GetOpt instance normaly
+// produced by the
+func MultiplexOptionSet(options *getoptions.GetOpt) {
+	options.StringVar(&_NGSFilterFile, "tag-list", _NGSFilterFile,
+		options.Alias("t"),
+		options.Description("File name of the NGSFilter file describing PCRs."))
+
+	options.BoolVar(&_ConservedError, "keep-errors", _ConservedError,
+		options.Description("Prints symbol counts."))
+
+	options.BoolVar(&_AllowsIndel, "with-indels", _AllowsIndel,
+		options.Description("Allows for indels during the primers matching."))
+
+	options.StringVar(&_UnidentifiedFile, "unidentified", _UnidentifiedFile,
+		options.Alias("u"),
+		options.Description("Filename used to store the sequences unassigned to any sample."))
+
+	options.IntVar(&_AllowedMismatch, "allowed-mismatches", _AllowedMismatch,
+		options.Alias("e"),
+		options.Description("Used to specify the number of errors allowed for matching primers."))
+
+	options.BoolVar(&_askTemplate, "template", _askTemplate,
+		options.Description("Print on the standard output an example of CSV configuration file."),
+	)
+
+}
+
+func OptionSet(options *getoptions.GetOpt) {
+	obiconvert.OptionSet(options)
+	MultiplexOptionSet(options)
+}
+
+func CLIAllowedMismatch() int {
+	return _AllowedMismatch
+}
+
+func CLIAllowsIndel() bool {
+	return _AllowsIndel
+}
+func CLIUnidentifiedFileName() string {
+	return _UnidentifiedFile
+}
+
+func CLIConservedErrors() bool {
+	return _UnidentifiedFile != "" || _ConservedError
+}
+
+func CLIHasNGSFilterFile() bool {
+	return _NGSFilterFile != ""
+}
+
+func CLINGSFIlter() (*obingslibrary.NGSLibrary, error) {
+	file, err := os.Open(_NGSFilterFile)
+
+	if err != nil {
+		return nil, fmt.Errorf("open file error: %v", err)
+	}
+
+	log.Infof("Reading NGSFilter file: %s", _NGSFilterFile)
+	ngsfiler, err := obiformats.ReadNGSFilter(file)
+
+	if err != nil {
+		return nil, fmt.Errorf("NGSfilter reading file error: %v", err)
+	}
+
+	return ngsfiler, nil
+}
+
+func CLIAskConfigTemplate() bool {
+	return _askTemplate
+}
+
+func CLIConfigTemplate() string {
+	return `experiment,sample,sample_tag,forward_primer,reverse_primer
+wolf_diet,13a_F730603,aattaac,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+wolf_diet,15a_F730814,gaagtag:gaatatc,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+wolf_diet,26a_F040644,gaatatc:-,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+wolf_diet,29a_F260619,-:-,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+`
+}

pkg/obitools/obitagpcr/pcrtag.go

@@ -33,12 +33,6 @@ func IPCRTagPESequencesBatch(iterator obiiter.IBioSequence,
 
 	newIter := obiiter.MakeIBioSequence()
 	newIter.MarkAsPaired()
-	newIter.Add(nworkers)
-
-	go func() {
-		newIter.WaitAndClose()
-		log.Printf("End of the sequence PCR Taging")
-	}()
 
 	f := func(iterator obiiter.IBioSequence, wid int) {
 		arena := obialign.MakePEAlignArena(150, 150)
@@ -128,16 +122,22 @@ func IPCRTagPESequencesBatch(iterator obiiter.IBioSequence,
 
 	log.Printf("Start of the sequence Pairing using %d workers\n", nworkers)
 
+	newIter.Add(nworkers)
 	for i := 1; i < nworkers; i++ {
 		go f(iterator.Split(), i)
 	}
 	go f(iterator, 0)
 
+	go func() {
+		newIter.WaitAndClose()
+		log.Printf("End of the sequence PCR Taging")
+	}()
+
 	iout := newIter
 
 	if !obimultiplex.CLIConservedErrors() {
 		log.Println("Discards unassigned sequences")
-		iout = iout.Rebatch(obioptions.CLIBatchSize())
+		iout = iout.FilterOn(obiseq.HasAttribute("demultiplex_error").Not(), obioptions.CLIBatchSize())
 	}
 
 	var unidentified obiiter.IBioSequence