change the model for representing paired reads and extend its usage to other commands

pkg/obichunk/unique.go

@@ -133,5 +133,5 @@ func IUniqueSequence(iterator obiiter.IBioSequence,
 		opts.BufferSize(),
 	)
 
-	return iMerged.Speed("Variants identified"), nil
+	return iMerged, nil
 }

pkg/obiformats/fastseq_write_fasta.go

@@ -69,7 +69,7 @@ func WriteFasta(iterator obiiter.IBioSequence,
 	options ...WithOption) (obiiter.IBioSequence, error) {
 	opt := MakeOptions(options)
 
-	file,_ = goutils.CompressStream(file,opt.CompressedFile(),opt.CloseFile())
+	file, _ = goutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
 
 	buffsize := iterator.BufferSize()
 	newIter := obiiter.MakeIBioSequence(buffsize)
@@ -136,7 +136,7 @@ func WriteFasta(iterator obiiter.IBioSequence,
 		}
 
 		file.Close()
-	
+
 		log.Debugln("End of the fasta file writing")
 		obiiter.UnregisterPipe()
 		waitWriter.Done()
@@ -156,7 +156,6 @@ func WriteFastaToFile(iterator obiiter.IBioSequence,
 	filename string,
 	options ...WithOption) (obiiter.IBioSequence, error) {
 
-
 	opt := MakeOptions(options)
 	flags := os.O_WRONLY | os.O_CREATE
 
@@ -164,7 +163,6 @@ func WriteFastaToFile(iterator obiiter.IBioSequence,
 		flags |= os.O_APPEND
 	}
 	file, err := os.OpenFile(filename, flags, 0660)
-	
 
 	if err != nil {
 		log.Fatalf("open file error: %v", err)
@@ -173,5 +171,18 @@ func WriteFastaToFile(iterator obiiter.IBioSequence,
 
 	options = append(options, OptionCloseFile())
 
-	return WriteFasta(iterator, file, options...)
+	iterator, err = WriteFasta(iterator, file, options...)
+
+	if opt.HaveToSavePaired() {
+		var revfile *os.File
+
+		revfile, err = os.OpenFile(opt.PairedFileName(), flags, 0660)
+		if err != nil {
+			log.Fatalf("open file error: %v", err)
+			return obiiter.NilIBioSequence, err
+		}
+		iterator, err = WriteFasta(iterator.PairedWith(), revfile, options...)
+	}
+
+	return iterator, err
 }

pkg/obiformats/fastseq_write_fastq.go

@@ -58,7 +58,7 @@ func WriteFastq(iterator obiiter.IBioSequence,
 	options ...WithOption) (obiiter.IBioSequence, error) {
 	opt := MakeOptions(options)
 
-	file,_ = goutils.CompressStream(file,opt.CompressedFile(),opt.CloseFile())
+	file, _ = goutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
 
 	buffsize := iterator.BufferSize()
 	newIter := obiiter.MakeIBioSequence(buffsize)
@@ -152,7 +152,7 @@ func WriteFastqToFile(iterator obiiter.IBioSequence,
 		flags |= os.O_APPEND
 	}
 	file, err := os.OpenFile(filename, flags, 0660)
-	
+
 	if err != nil {
 		log.Fatalf("open file error: %v", err)
 		return obiiter.NilIBioSequence, err
@@ -160,5 +160,18 @@ func WriteFastqToFile(iterator obiiter.IBioSequence,
 
 	options = append(options, OptionCloseFile())
 
-	return WriteFastq(iterator, file, options...)
+	iterator, err = WriteFastq(iterator, file, options...)
+
+	if opt.HaveToSavePaired() {
+		var revfile *os.File
+
+		revfile, err = os.OpenFile(opt.PairedFileName(), flags, 0660)
+		if err != nil {
+			log.Fatalf("open file error: %v", err)
+			return obiiter.NilIBioSequence, err
+		}
+		iterator, err = WriteFastq(iterator.PairedWith(), revfile, options...)
+	}
+
+	return iterator, err
 }

pkg/obiformats/options.go

@@ -15,6 +15,11 @@ type __options__ struct {
 	closefile             bool
 	appendfile            bool
 	compressed            bool
+	csv_ids               bool
+	cvs_sequence          bool
+	csv_definition        bool
+	csv_separator         string
+	paired_filename       string
 }
 
 type Options struct {
@@ -35,6 +40,11 @@ func MakeOptions(setters []WithOption) Options {
 		closefile:             false,
 		appendfile:            false,
 		compressed:            false,
+		csv_ids:               true,
+		csv_definition:        false,
+		cvs_sequence:          true,
+		csv_separator:         ",",
+		paired_filename: "",
 	}
 
 	opt := Options{&o}
@@ -86,6 +96,18 @@ func (opt Options) CompressedFile() bool {
 	return opt.pointer.compressed
 }
 
+func (opt Options) CSVIds() bool {
+	return opt.pointer.csv_ids
+}
+
+func (opt Options) HaveToSavePaired() bool {
+	return opt.pointer.paired_filename != ""
+}
+
+func (opt Options) PairedFileName() string {
+	return opt.pointer.paired_filename
+}
+
 func OptionsBufferSize(size int) WithOption {
 	f := WithOption(func(opt Options) {
 		opt.pointer.buffer_size = size
@@ -216,3 +238,12 @@ func OptionsWithoutProgressBar() WithOption {
 
 	return f
 }
+
+func WritePairedReadsTo(filename string) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.paired_filename = filename
+	})
+
+	return f
+}
+

pkg/obiformats/universal_write.go

@@ -69,5 +69,19 @@ func WriteSequencesToFile(iterator obiiter.IBioSequence,
 	}
 
 	options = append(options, OptionCloseFile())
-	return WriteSequence(iterator, file, options...)
+
+	iterator, err = WriteSequence(iterator, file, options...)
+
+	if opt.HaveToSavePaired() {
+		var revfile *os.File
+
+		revfile, err = os.OpenFile(opt.PairedFileName(), flags, 0660)
+		if err != nil {
+			log.Fatalf("open file error: %v", err)
+			return obiiter.NilIBioSequence, err
+		}
+		iterator, err = WriteSequence(iterator.PairedWith(), revfile, options...)
+	}
+
+	return iterator, err
 }

pkg/obiiter/batchiterator.go

@@ -46,6 +46,7 @@ type _IBioSequence struct {
 	batch_size      int32
 	sequence_format string
 	finished        *abool.AtomicBool
+	paired          bool
 }
 
 type IBioSequence struct {
@@ -73,6 +74,7 @@ func MakeIBioSequence(sizes ...int) IBioSequence {
 		batch_size:      -1,
 		sequence_format: "",
 		finished:        abool.New(),
+		paired:          false,
 	}
 
 	waiting := sync.WaitGroup{}
@@ -199,6 +201,11 @@ func (iterator IBioSequence) Split() IBioSequence {
 	i.lock = &lock
 
 	newIter := IBioSequence{&i}
+
+	if iterator.IsPaired() {
+		newIter.MarkAsPaired()
+	}
+
 	return newIter
 }
 
@@ -270,6 +277,7 @@ func (iterator IBioSequence) Finished() bool {
 	return iterator.pointer.finished.IsSet()
 }
 
+// Sorting the batches of sequences.
 func (iterator IBioSequence) SortBatches(sizes ...int) IBioSequence {
 	buffsize := iterator.BufferSize()
 
@@ -311,6 +319,10 @@ func (iterator IBioSequence) SortBatches(sizes ...int) IBioSequence {
 		newIter.Done()
 	}()
 
+	if iterator.IsPaired() {
+		newIter.MarkAsPaired()
+	}
+
 	return newIter
 
 }
@@ -321,6 +333,11 @@ func (iterator IBioSequence) Concat(iterators ...IBioSequence) IBioSequence {
 		return iterator
 	}
 
+	allPaired := iterator.IsPaired()
+	for _, i := range iterators {
+		allPaired = allPaired && i.IsPaired()
+	}
+
 	buffsize := iterator.BufferSize()
 	newIter := MakeIBioSequence(buffsize)
 
@@ -357,6 +374,10 @@ func (iterator IBioSequence) Concat(iterators ...IBioSequence) IBioSequence {
 		newIter.Done()
 	}()
 
+	if allPaired {
+		newIter.MarkAsPaired()
+	}
+
 	return newIter
 }
 
@@ -368,6 +389,12 @@ func (iterator IBioSequence) Pool(iterators ...IBioSequence) IBioSequence {
 		return iterator
 	}
 
+	allPaired := iterator.IsPaired()
+
+	for _, i := range iterators {
+		allPaired = allPaired && i.IsPaired()
+	}
+
 	nextCounter := goutils.AtomicCounter()
 	buffsize := iterator.BufferSize()
 	newIter := MakeIBioSequence(buffsize)
@@ -392,6 +419,10 @@ func (iterator IBioSequence) Pool(iterators ...IBioSequence) IBioSequence {
 		go ff(i)
 	}
 
+	if allPaired {
+		newIter.MarkAsPaired()
+	}
+
 	return newIter
 }
 
@@ -441,6 +472,10 @@ func (iterator IBioSequence) Rebatch(size int, sizes ...int) IBioSequence {
 
 	}()
 
+	if iterator.IsPaired() {
+		newIter.MarkAsPaired()
+	}
+
 	return newIter
 }
 
@@ -492,47 +527,6 @@ func (iterator IBioSequence) Count(recycle bool) (int, int, int) {
 	return variants, reads, nucleotides
 }
 
-func (iterator IBioSequence) PairWith(reverse IBioSequence,
-	sizes ...int) IPairedBioSequenceBatch {
-	buffsize := iterator.BufferSize()
-	batchsize := 5000
-
-	if len(sizes) > 0 {
-		batchsize = sizes[0]
-	}
-
-	if len(sizes) > 1 {
-		buffsize = sizes[1]
-	}
-
-	iterator = iterator.Rebatch(batchsize)
-	reverse = reverse.Rebatch(batchsize)
-
-	newIter := MakeIPairedBioSequenceBatch(buffsize)
-
-	newIter.Add(1)
-
-	go func() {
-		newIter.WaitAndClose()
-		log.Println("End of association of paired reads")
-	}()
-
-	log.Println("Start association of paired reads")
-	go func() {
-		for iterator.Next() {
-			if !reverse.Next() {
-				log.Panicln("Etrange reverse pas prêt")
-			}
-			newIter.Channel() <- MakePairedBioSequenceBatch(iterator.Get(),
-				reverse.Get())
-		}
-
-		newIter.Done()
-	}()
-
-	return newIter
-}
-
 // A function that takes a predicate and returns two IBioSequenceBatch iterators.
 // Sequences extracted from the input iterator are distributed among both the
 // iterator following the predicate value.
@@ -599,6 +593,10 @@ func (iterator IBioSequence) DivideOn(predicate obiseq.SequencePredicate,
 		falseIter.Done()
 	}()
 
+	if iterator.IsPaired() {
+		trueIter.MarkAsPaired()
+		falseIter.MarkAsPaired()
+	}
 	return trueIter, falseIter
 }
 
@@ -654,6 +652,71 @@ func (iterator IBioSequence) FilterOn(predicate obiseq.SequencePredicate,
 
 	go ff(iterator)
 
+	if iterator.IsPaired() {
+		trueIter.MarkAsPaired()
+	}
+
+	return trueIter.Rebatch(size)
+}
+
+func (iterator IBioSequence) FilterAnd(predicate obiseq.SequencePredicate,
+	size int, sizes ...int) IBioSequence {
+	buffsize := iterator.BufferSize()
+	nworkers := 4
+
+	if len(sizes) > 0 {
+		nworkers = sizes[0]
+	}
+
+	if len(sizes) > 1 {
+		buffsize = sizes[1]
+	}
+
+	trueIter := MakeIBioSequence(buffsize)
+
+	trueIter.Add(nworkers)
+
+	go func() {
+		trueIter.WaitAndClose()
+	}()
+
+	ff := func(iterator IBioSequence) {
+		// iterator = iterator.SortBatches()
+
+		for iterator.Next() {
+			seqs := iterator.Get()
+			slice := seqs.slice
+			j := 0
+			for _, s := range slice {
+				good := predicate(s)
+				if s.IsPaired() {
+					good = good && predicate(s.PairedWith())
+				}
+				if good {
+					slice[j] = s
+					j++
+				} else {
+					s.Recycle()
+				}
+			}
+
+			seqs.slice = slice[:j]
+			trueIter.pointer.channel <- seqs
+		}
+
+		trueIter.Done()
+	}
+
+	for i := 1; i < nworkers; i++ {
+		go ff(iterator.Split())
+	}
+
+	go ff(iterator)
+
+	if iterator.IsPaired() {
+		trueIter.MarkAsPaired()
+	}
+
 	return trueIter.Rebatch(size)
 }
 
@@ -673,13 +736,14 @@ func (iterator IBioSequence) Load() obiseq.BioSequenceSlice {
 
 // It takes a slice of BioSequence objects, and returns an iterator that will return batches of
 // BioSequence objects
+
 func IBatchOver(data obiseq.BioSequenceSlice,
 	size int, sizes ...int) IBioSequence {
 
 	buffsize := 0
 
 	if len(sizes) > 0 {
-		buffsize = sizes[1]
+		buffsize = sizes[0]
 	}
 
 	newIter := MakeIBioSequence(buffsize)
@@ -706,5 +770,8 @@ func IBatchOver(data obiseq.BioSequenceSlice,
 		newIter.Done()
 	}()
 
+	if data.IsPaired() {
+		newIter.MarkAsPaired()
+	}
 	return newIter
 }

pkg/obiiter/paired.go

@@ -0,0 +1,95 @@
+package obiiter
+
+import (
+	"log"
+)
+
+func (b BioSequenceBatch) IsPaired() bool {
+	return b.slice.IsPaired()
+}
+
+func (b BioSequenceBatch) PairedWith() BioSequenceBatch {
+	return MakeBioSequenceBatch(b.order,
+		*b.slice.PairedWith())
+
+}
+
+func (b *BioSequenceBatch) PairTo(p *BioSequenceBatch) {
+
+	if b.order != p.order {
+		log.Fatalf("both batches are not synchronized : (%d,%d)",
+			b.order, p.order,
+		)
+	}
+
+	b.slice.PairTo(&p.slice)
+
+}
+
+func (b *BioSequenceBatch) UnPair() {
+	b.slice.UnPair()
+}
+
+func (iter IBioSequence) MarkAsPaired() {
+	iter.pointer.paired = true
+}
+
+func (iter IBioSequence) PairTo(p IBioSequence) IBioSequence {
+
+	newIter := MakeIBioSequence()
+
+	iter = iter.SortBatches()
+	p = p.SortBatches()
+
+	newIter.Add(1)
+
+	go func() {
+		newIter.WaitAndClose()
+	}()
+
+	go func() {
+
+		for iter.Next() {
+			p.Next()
+			batch := iter.Get()
+			pbatch := p.Get()
+			batch.PairTo(&pbatch)
+			newIter.Push(batch)
+		}
+
+		newIter.Done()
+	}()
+
+	newIter.MarkAsPaired()
+	return newIter
+
+}
+
+func (iter IBioSequence) PairedWith() IBioSequence {
+
+	newIter := MakeIBioSequence()
+
+	newIter.Add(1)
+
+	go func() {
+		newIter.WaitAndClose()
+	}()
+
+	go func() {
+
+		for iter.Next() {
+			batch := iter.Get().PairedWith()
+			newIter.Push(batch)
+		}
+
+		newIter.Done()
+	}()
+
+	newIter.MarkAsPaired()
+	return newIter
+
+}
+
+func (iter IBioSequence) IsPaired() bool {
+	return iter.pointer.paired
+}

pkg/obiiter/pairedbatchiterator.go

@@ -1,239 +0,0 @@
-package obiiter
-
-import (
-	"sync"
-	"time"
-
-	log "github.com/sirupsen/logrus"
-
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
-)
-
-type PairedBioSequenceBatch struct {
-	forward obiseq.BioSequenceSlice
-	reverse obiseq.BioSequenceSlice
-	order   int
-}
-
-var NilPairedBioSequenceBatch = PairedBioSequenceBatch{nil, nil, -1}
-
-func MakePairedBioSequenceBatch(forward, reverse BioSequenceBatch) PairedBioSequenceBatch {
-	if forward.order != reverse.order {
-		log.Fatalf("Forward order : %d and reverse order : %d are not matching",
-			forward.order, reverse.order)
-	}
-
-	for i := range reverse.slice {
-		reverse.slice[i].ReverseComplement(true)
-	}
-
-	return PairedBioSequenceBatch{
-		forward: forward.slice,
-		reverse: reverse.slice,
-		order:   forward.order,
-	}
-}
-
-func (batch PairedBioSequenceBatch) Order() int {
-	return batch.order
-}
-
-func (batch PairedBioSequenceBatch) Reorder(newOrder int) PairedBioSequenceBatch {
-	batch.order = newOrder
-	return batch
-}
-
-func (batch PairedBioSequenceBatch) Len() int {
-	return len(batch.forward)
-}
-
-func (batch PairedBioSequenceBatch) Forward() obiseq.BioSequenceSlice {
-	return batch.forward
-}
-
-func (batch PairedBioSequenceBatch) Reverse() obiseq.BioSequenceSlice {
-	return batch.reverse
-}
-
-func (batch PairedBioSequenceBatch) IsNil() bool {
-	return batch.forward == nil
-}
-
-// Structure implementing an iterator over bioseq.BioSequenceBatch
-// based on a channel.
-type __ipairedbiosequencebatch__ struct {
-	channel     chan PairedBioSequenceBatch
-	current     PairedBioSequenceBatch
-	pushBack    bool
-	all_done    *sync.WaitGroup
-	buffer_size int
-	finished    bool
-	p_finished  *bool
-}
-
-type IPairedBioSequenceBatch struct {
-	pointer *__ipairedbiosequencebatch__
-}
-
-var NilIPairedBioSequenceBatch = IPairedBioSequenceBatch{pointer: nil}
-
-func MakeIPairedBioSequenceBatch(sizes ...int) IPairedBioSequenceBatch {
-	buffsize := 1
-
-	if len(sizes) > 0 {
-		buffsize = sizes[0]
-	}
-
-	i := __ipairedbiosequencebatch__{
-		channel:     make(chan PairedBioSequenceBatch, buffsize),
-		current:     NilPairedBioSequenceBatch,
-		pushBack:    false,
-		buffer_size: buffsize,
-		finished:    false,
-		p_finished:  nil,
-	}
-
-	i.p_finished = &i.finished
-	waiting := sync.WaitGroup{}
-	i.all_done = &waiting
-	ii := IPairedBioSequenceBatch{&i}
-
-	RegisterAPipe()
-	return ii
-}
-
-func (iterator IPairedBioSequenceBatch) Add(n int) {
-	iterator.pointer.all_done.Add(n)
-}
-
-func (iterator IPairedBioSequenceBatch) Done() {
-	iterator.pointer.all_done.Done()
-}
-
-func (iterator IPairedBioSequenceBatch) Wait() {
-	iterator.pointer.all_done.Wait()
-}
-
-func (iterator IPairedBioSequenceBatch) Channel() chan PairedBioSequenceBatch {
-	return iterator.pointer.channel
-}
-
-func (iterator IPairedBioSequenceBatch) Close() {
-	close(iterator.pointer.channel)
-	UnregisterPipe()
-}
-
-func (iterator IPairedBioSequenceBatch) WaitAndClose() {
-	iterator.Wait()
-
-	for len(iterator.Channel()) > 0 {
-		time.Sleep(time.Millisecond)
-	}
-
-	iterator.Close()
-}
-
-func (iterator IPairedBioSequenceBatch) IsNil() bool {
-	return iterator.pointer == nil
-}
-
-func (iterator IPairedBioSequenceBatch) BufferSize() int {
-	return iterator.pointer.buffer_size
-}
-
-func (iterator IPairedBioSequenceBatch) Split() IPairedBioSequenceBatch {
-	i := __ipairedbiosequencebatch__{
-		channel:     iterator.pointer.channel,
-		current:     NilPairedBioSequenceBatch,
-		pushBack:    false,
-		all_done:    iterator.pointer.all_done,
-		buffer_size: iterator.pointer.buffer_size,
-		finished:    false,
-		p_finished:  iterator.pointer.p_finished}
-	newIter := IPairedBioSequenceBatch{&i}
-	return newIter
-}
-
-func (iterator IPairedBioSequenceBatch) Next() bool {
-	if *(iterator.pointer.p_finished) {
-		return false
-	}
-
-	if iterator.pointer.pushBack {
-		iterator.pointer.pushBack = false
-		return true
-	}
-
-	next, ok := (<-iterator.pointer.channel)
-
-	if ok {
-		iterator.pointer.current = next
-		return true
-	}
-
-	iterator.pointer.current = NilPairedBioSequenceBatch
-	*iterator.pointer.p_finished = true
-	return false
-}
-
-func (iterator IPairedBioSequenceBatch) PushBack() {
-	if !iterator.pointer.current.IsNil() {
-		iterator.pointer.pushBack = true
-	}
-}
-
-// The 'Get' method returns the instance of BioSequenceBatch
-// currently pointed by the iterator. You have to use the
-// 'Next' method to move to the next entry before calling
-// 'Get' to retreive the following instance.
-func (iterator IPairedBioSequenceBatch) Get() PairedBioSequenceBatch {
-	return iterator.pointer.current
-}
-
-// Finished returns 'true' value if no more data is available
-// from the iterator.
-func (iterator IPairedBioSequenceBatch) Finished() bool {
-	return *iterator.pointer.p_finished
-}
-
-func (iterator IPairedBioSequenceBatch) SortBatches(sizes ...int) IPairedBioSequenceBatch {
-	buffsize := iterator.BufferSize()
-
-	if len(sizes) > 0 {
-		buffsize = sizes[0]
-	}
-
-	newIter := MakeIPairedBioSequenceBatch(buffsize)
-
-	newIter.Add(1)
-
-	go func() {
-		newIter.Wait()
-		close(newIter.pointer.channel)
-	}()
-
-	next_to_send := 0
-	received := make(map[int]PairedBioSequenceBatch)
-	go func() {
-		for iterator.Next() {
-			batch := iterator.Get()
-			if batch.order == next_to_send {
-				newIter.pointer.channel <- batch
-				next_to_send++
-				batch, ok := received[next_to_send]
-				for ok {
-					newIter.pointer.channel <- batch
-					delete(received, next_to_send)
-					next_to_send++
-					batch, ok = received[next_to_send]
-				}
-			} else {
-				received[batch.order] = batch
-			}
-		}
-		newIter.Done()
-	}()
-
-	return newIter
-
-}

pkg/obiiter/pipe.go

@@ -40,5 +40,10 @@ func (input IBioSequence) CopyTee() (IBioSequence, IBioSequence) {
 		}
 	}()
 
+	if input.IsPaired() {
+		first.MarkAsPaired()
+		second.MarkAsPaired()
+	}
+
 	return first, second
 }

pkg/obiiter/speed.go

@@ -3,6 +3,7 @@ package obiiter
 import (
 	"fmt"
 	"os"
+	"time"
 
 	"github.com/schollz/progressbar/v3"
 )
@@ -45,18 +46,29 @@ func (iterator IBioSequence) Speed(message ...string) IBioSequence {
 	bar := progressbar.NewOptions(-1, pbopt...)
 
 	go func() {
+		c := 0
+		start := time.Now()
 
 		for iterator.Next() {
 			batch := iterator.Get()
-			l := batch.Len()
+			c += batch.Len()
 			newIter.Push(batch)
-			bar.Add(l)
+			elapsed := time.Since(start)
+			if elapsed > (time.Millisecond * 100) {
+				bar.Add(c)
+				c = 0
+				start = time.Now()
+			}
 		}
 
 		fmt.Fprintln(os.Stderr)
 		newIter.Done()
 	}()
 
+	if iterator.IsPaired() {
+		newIter.MarkAsPaired()
+	}
+	
 	return newIter
 }
 

pkg/obiiter/workers.go

@@ -54,6 +54,10 @@ func (iterator IBioSequence) MakeIWorker(worker obiseq.SeqWorker, sizes ...int)
 	}
 	go f(iterator)
 
+	if iterator.IsPaired() {
+		newIter.MarkAsPaired()
+	}
+
 	return newIter
 }
 
@@ -99,6 +103,10 @@ func (iterator IBioSequence) MakeIConditionalWorker(predicate obiseq.SequencePre
 	}
 	go f(iterator)
 
+	if iterator.IsPaired() {
+		newIter.MarkAsPaired()
+	}
+
 	return newIter
 }
 
@@ -138,6 +146,10 @@ func (iterator IBioSequence) MakeISliceWorker(worker obiseq.SeqSliceWorker, size
 	}
 	go f(iterator)
 
+	if iterator.IsPaired() {
+		newIter.MarkAsPaired()
+	}
+
 	return newIter
 }
 

pkg/obioptions/options.go

@@ -11,7 +11,7 @@ import (
 )
 
 var _Debug = false
-var _ParallelWorkers = runtime.NumCPU() - 1
+var _ParallelWorkers = runtime.NumCPU() * 2 - 1
 var _MaxAllowedCPU = runtime.NumCPU()
 var _BufferSize = 1
 var _BatchSize = 5000
@@ -19,7 +19,10 @@ var _BatchSize = 5000
 type ArgumentParser func([]string) (*getoptions.GetOpt, []string, error)
 
 func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser {
+
 	options := getoptions.New()
+	options.SetMode(getoptions.Bundling)
+	options.SetUnknownMode(getoptions.Fail)
 	options.Bool("help", false, options.Alias("h", "?"))
 	options.BoolVar(&_Debug, "debug", false)
 
@@ -28,6 +31,7 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 		options.Description("Number of parallele threads computing the result"))
 
 	options.IntVar(&_MaxAllowedCPU, "max-cpu", _MaxAllowedCPU,
+		options.GetEnv("OBIMAXCPU"),
 		options.Description("Number of parallele threads computing the result"))
 
 	for _, o := range optionset {
@@ -42,6 +46,10 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 		runtime.GOMAXPROCS(_MaxAllowedCPU)
 		if options.Called("max-cpu") {
 			log.Printf("CPU number limited to %d", _MaxAllowedCPU)
+			if ! options.Called("workers") {
+				_ParallelWorkers=_MaxAllowedCPU * 2 - 1
+				log.Printf("Number of workers set %d", _ParallelWorkers)
+			}
 		}
 
 		if options.Called("no-singleton") {

pkg/obiseq/biosequence.go

@@ -55,6 +55,7 @@ type BioSequence struct {
 	sequence    []byte // The sequence itself, it is accessible by the methode Sequence
 	qualities   []byte // The quality scores of the sequence.
 	feature     []byte
+	paired      *BioSequence // A pointer to the paired sequence
 	annotations Annotation
 }
 
@@ -69,6 +70,7 @@ func MakeEmptyBioSequence() BioSequence {
 		sequence:    nil,
 		qualities:   nil,
 		feature:     nil,
+		paired:      nil,
 		annotations: nil,
 	}
 }
@@ -275,3 +277,4 @@ func (s *BioSequence) WriteByte(data byte) error {
 func (s *BioSequence) Clear() {
 	s.sequence = s.sequence[0:0]
 }
+

pkg/obiseq/biosequenceslice.go

@@ -23,7 +23,7 @@ func NewBioSequenceSlice(size ...int) *BioSequenceSlice {
 	slice := _BioSequenceSlicePool.Get().(*BioSequenceSlice)
 	if len(size) > 0 {
 		s := size[0]
-		slice.InsureCapacity(s)
+		slice = slice.InsureCapacity(s)
 		(*slice)=(*slice)[0:s]
 	}
 	return slice

pkg/obiseq/paired_reads.go

@@ -0,0 +1,58 @@
+package obiseq
+
+import log "github.com/sirupsen/logrus"
+
+func (s *BioSequence) IsPaired() bool {
+	return s.paired != nil
+}
+
+func (s *BioSequence) PairedWith() *BioSequence {
+	return s.paired
+}
+
+func (s *BioSequence) PairTo(p *BioSequence) {
+	s.paired = p
+	if p != nil {
+		p.paired = s
+	}
+}
+
+func (s *BioSequence) UnPair() {
+	if s.paired != nil {
+		s.paired.paired = nil
+	}
+	s.paired = nil
+}
+
+func (s *BioSequenceSlice) IsPaired() bool {
+	return (*s)[0].paired != nil
+}
+
+func (s *BioSequenceSlice) PairedWith() *BioSequenceSlice {
+	ps := NewBioSequenceSlice(len(*s))
+	for i, seq := range *s {
+		(*ps)[i] = seq.PairedWith()
+	}
+
+	return ps
+}
+
+func (s *BioSequenceSlice) PairTo(p *BioSequenceSlice) {
+
+	if len(*s) != len(*p) {
+		log.Fatalf("Pairing of iterators: both batches have not the same length : (%d,%d)",
+			len(*s), len(*p),
+		)
+	}
+
+	for i, seq := range *s {
+		seq.PairTo((*p)[i])
+	}
+
+}
+
+func (s *BioSequenceSlice) UnPair() {
+	for _, seq := range *s {
+		seq.UnPair()
+	}
+}

pkg/obiseq/predicate.go

@@ -11,6 +11,61 @@ import (
 
 type SequencePredicate func(*BioSequence) bool
 
+type SeqPredicateMode int
+
+const (
+	ForwardOnly SeqPredicateMode = iota
+	ReverseOnly
+	And
+	Or
+	AndNot
+	Xor
+)
+
+func (predicate SequencePredicate) PredicateOnPaired(ifnotpaired bool) SequencePredicate {
+	if predicate == nil {
+		return nil
+	}
+
+	p := func(sequence *BioSequence) bool {
+		if sequence.IsPaired() {
+			return predicate(sequence.PairedWith())
+		}
+		return ifnotpaired
+	}
+
+	return p
+}
+
+func (predicate SequencePredicate) PairedPredicat(mode SeqPredicateMode) SequencePredicate {
+	if predicate == nil {
+		return nil
+	}
+
+	p := func(sequence *BioSequence) bool {
+		good := predicate(sequence)
+
+		if sequence.IsPaired() && mode != ForwardOnly {
+			pgood := predicate(sequence.PairedWith())
+			switch mode {
+			case ReverseOnly:
+				good = pgood
+			case And:
+				good = good && pgood
+			case Or:
+				good = good || pgood
+			case AndNot:
+				good = good && !pgood
+			case Xor:
+				good = (good || pgood) && !(good && pgood)
+			}
+		}
+		return good
+	}
+
+	return p
+}
+
 func (predicate1 SequencePredicate) And(predicate2 SequencePredicate) SequencePredicate {
 	switch {
 	case predicate1 == nil:
@@ -209,8 +264,8 @@ func ExpressionPredicat(expression string) SequencePredicate {
 	f := func(sequence *BioSequence) bool {
 		value, err := exp.EvalBool(context.Background(),
 			map[string]interface{}{
-				"annotations":     sequence.Annotations(),
-				"sequence":  sequence,
+				"annotations": sequence.Annotations(),
+				"sequence":    sequence,
 			},
 		)
 
@@ -225,4 +280,3 @@ func ExpressionPredicat(expression string) SequencePredicate {
 
 	return f
 }
-

pkg/obitools/obiconvert/options.go

@@ -27,6 +27,9 @@ var __output_solexa_quality__ = false
 var __no_progress_bar__ = false
 var __compressed__ = false
 
+var __output_file_name__ = "-"
+var __paired_file_name__ = ""
+
 func InputOptionSet(options *getoptions.GetOpt) {
 	// options.IntVar(&__skipped_entries__, "skip", __skipped_entries__,
 	// 	options.Description("The N first sequence records of the file are discarded from the analysis and not reported to the output file."))
@@ -73,15 +76,29 @@ func OutputOptionSet(options *getoptions.GetOpt) {
 	options.BoolVar(&__no_progress_bar__, "no-progressbar", false,
 		options.Description("Disable the progress bar printing"))
 
-	options.BoolVar(&__compressed__, "--compress", false,
+	options.BoolVar(&__compressed__, "compress", false,
 		options.Alias("Z"),
 		options.Description("Output is compressed"))
 
+	options.StringVar(&__output_file_name__, "out", __output_file_name__,
+		options.Alias("o"),
+		options.ArgName("FILENAME"),
+		options.Description("Filename used for saving the output"),
+	)
+
+}
+
+func PairedFilesOptionSet(options *getoptions.GetOpt) {
+	options.StringVar(&__paired_file_name__, "paired-with", __paired_file_name__,
+		options.ArgName("FILENAME"),
+		options.Description("Filename containing the paired reads"),
+	)
 }
 
 func OptionSet(options *getoptions.GetOpt) {
 	InputOptionSet(options)
 	OutputOptionSet(options)
+	PairedFilesOptionSet(options)
 }
 
 // Returns true if the number of reads described in the
@@ -170,3 +187,14 @@ func CLIOutputQualityShift() int {
 func CLIProgressBar() bool {
 	return !__no_progress_bar__
 }
+
+func CLIOutPutFileName() string {
+	return __output_file_name__
+}
+
+func CLIHasPairedFile() bool {
+	return __paired_file_name__ != ""
+}
+func CLIPairedFileName() string {
+	return __paired_file_name__
+}

pkg/obitools/obiconvert/sequence_reader.go

@@ -67,7 +67,7 @@ func _ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
 	return list_of_files, nil
 }
 
-func ReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
+func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 	var iterator obiiter.IBioSequence
 	var reader func(string, ...obiformats.WithOption) (obiiter.IBioSequence, error)
 
@@ -142,6 +142,17 @@ func ReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 			if err != nil {
 				return obiiter.NilIBioSequence, err
 			}
+
+			if CLIPairedFileName() != "" {
+				ip, err := reader(CLIPairedFileName(), opts...)
+
+				if err != nil {
+					return obiiter.NilIBioSequence, err
+				}
+
+				iterator = iterator.PairTo(ip)
+			}
+
 		}
 
 		// list_of_files = list_of_files[1:]

pkg/obitools/obiconvert/sequence_writer.go

@@ -1,6 +1,9 @@
 package obiconvert
 
 import (
+	"path/filepath"
+	"strings"
+
 	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
@@ -8,6 +11,27 @@ import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
 )
 
+func BuildPairedFileNames(filename string) (string, string) {
+
+	dir, name := filepath.Split(filename)
+	parts := strings.SplitN(name, ".", 2)
+
+	forward := parts[0] + "_R1"
+	reverse := parts[0] + "_R2"
+
+	if parts[1] != "" {
+		suffix := "." + parts[1]
+		forward += suffix
+		reverse += suffix
+	}
+
+	if dir != "" {
+		forward = filepath.Join(dir, forward)
+		reverse = filepath.Join(dir, reverse)
+	}
+
+	return forward, reverse
+}
 func CLIWriteBioSequences(iterator obiiter.IBioSequence,
 	terminalAction bool, filenames ...string) (obiiter.IBioSequence, error) {
 
@@ -45,7 +69,32 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
 
 	var err error
 
-	if len(filenames) == 0 {
+	// No file names are specified or it is "-" : the output is done on stdout
+
+	if CLIOutPutFileName() != "-" || (len(filenames) > 0 && filenames[0] != "-") {
+		var fn string
+
+		if len(filenames) == 0 {
+			fn = CLIOutPutFileName()
+		} else {
+			fn = filenames[0]
+		}
+
+		if iterator.IsPaired() {
+			var reverse string
+			fn, reverse = BuildPairedFileNames(fn)
+			opts = append(opts, obiformats.WritePairedReadsTo(reverse))
+		}
+
+		switch CLIOutputFormat() {
+		case "fastq":
+			newIter, err = obiformats.WriteFastqToFile(iterator, fn, opts...)
+		case "fasta":
+			newIter, err = obiformats.WriteFastaToFile(iterator, fn, opts...)
+		default:
+			newIter, err = obiformats.WriteSequencesToFile(iterator, fn, opts...)
+		}
+	} else {
 		switch CLIOutputFormat() {
 		case "fastq":
 			newIter, err = obiformats.WriteFastqToStdout(iterator, opts...)
@@ -54,15 +103,6 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
 		default:
 			newIter, err = obiformats.WriteSequencesToStdout(iterator, opts...)
 		}
-	} else {
-		switch CLIOutputFormat() {
-		case "fastq":
-			newIter, err = obiformats.WriteFastqToFile(iterator, filenames[0], opts...)
-		case "fasta":
-			newIter, err = obiformats.WriteFastaToFile(iterator, filenames[0], opts...)
-		default:
-			newIter, err = obiformats.WriteSequencesToFile(iterator, filenames[0], opts...)
-		}
 	}
 
 	if err != nil {

pkg/obitools/obigrep/grep.go

@@ -8,11 +8,15 @@ import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
 )
 
-func IFilterSequence(iterator obiiter.IBioSequence) obiiter.IBioSequence {
+func CLIFilterSequence(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 	var newIter obiiter.IBioSequence
 
 	predicate := CLISequenceSelectionPredicate()
 
+	if obiconvert.CLIHasPairedFile() {
+		predicate = predicate.PairedPredicat(CLIPairedReadMode())
+	}
+
 	if predicate != nil {
 		if CLISaveDiscardedSequences() {
 			var discarded obiiter.IBioSequence

pkg/obitools/obigrep/options.go

@@ -40,6 +40,8 @@ var _AttributePatterns = make(map[string]string, 0)
 var _InvertMatch = false
 var _SaveRejected = ""
 
+var _PairedMode = "forward"
+
 func TaxonomySelectionOptionSet(options *getoptions.GetOpt) {
 
 	options.StringVar(&_Taxdump, "taxdump", _Taxdump,
@@ -135,6 +137,11 @@ func SequenceSelectionOptionSet(options *getoptions.GetOpt) {
 			"Several -a options can be used on the same command line and in this last case, the selected "+
 			"sequence records will match all constraints."))
 
+	options.StringVar(&_PairedMode, "paired-mode", _PairedMode,
+		options.ArgName("forward|reverse|and|or|andnot|xor"),
+		options.Description("If paired reads are passed to obibrep, that option determines how the conditions "+
+			"are applied to both reads."),
+	)
 }
 
 // OptionSet adds to the basic option set every options declared for
@@ -412,3 +419,24 @@ func CLISaveDiscardedSequences() bool {
 func CLIDiscardedFileName() string {
 	return _SaveRejected
 }
+
+func CLIPairedReadMode() obiseq.SeqPredicateMode {
+	switch _PairedMode {
+	case "forward":
+		return obiseq.ForwardOnly
+	case "reverse":
+		return obiseq.ReverseOnly
+	case "and":
+		return obiseq.And
+	case "or":
+		return obiseq.Or
+	case "andnot":
+		return obiseq.AndNot
+	case "xor":
+		return obiseq.Xor
+	default:
+		log.Fatalf("Paired reads mode must be forward, reverse, and, or, andnot, or xor (%s)", _PairedMode)
+	}
+
+	return obiseq.ForwardOnly
+}

pkg/obitools/obipairing/options.go

@@ -6,8 +6,8 @@ import (
 	"github.com/DavidGamba/go-getoptions"
 )
 
-var _ForwardFiles = make([]string, 0, 10)
-var _ReverseFiles = make([]string, 0, 10)
+var _ForwardFile = ""
+var _ReverseFile = ""
 var _Delta = 5
 var _MinOverlap = 20
 var _GapPenality = float64(2.0)
@@ -15,15 +15,15 @@ var _WithoutStats = false
 var _MinIdentity = 0.9
 
 func PairingOptionSet(options *getoptions.GetOpt) {
-	options.StringSliceVar(&_ForwardFiles, "forward-reads",
-		1, 1000,
+	options.StringVar(&_ForwardFile, "forward-reads", "",
 		options.Alias("F"),
-		options.Required("You must provide at least one forward file"),
+		options.ArgName("FILENAME_F"),
+		options.Required("You must provide at a forward file"),
 		options.Description("The file names containing the forward reads"))
-	options.StringSliceVar(&_ReverseFiles, "reverse-reads",
-		1, 1000,
+	options.StringVar(&_ReverseFile, "reverse-reads", "",
 		options.Alias("R"),
-		options.Required("You must provide at least one reverse file"),
+		options.ArgName("FILENAME_R"),
+		options.Required("You must provide a reverse file"),
 		options.Description("The file names containing the reverse reads"))
 	options.IntVar(&_Delta, "delta", _Delta,
 		options.Alias("D"),
@@ -42,42 +42,43 @@ func PairingOptionSet(options *getoptions.GetOpt) {
 }
 
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OutputOptionSet(options)
+	obiconvert.InputOptionSet(options)
 	PairingOptionSet(options)
 }
 
-func IBatchPairedSequence() (obiiter.IPairedBioSequenceBatch, error) {
-	forward, err := obiconvert.ReadBioSequences(_ForwardFiles...)
+func CLIPairedSequence() (obiiter.IBioSequence, error) {
+	forward, err := obiconvert.CLIReadBioSequences(_ForwardFile)
 	if err != nil {
-		return obiiter.NilIPairedBioSequenceBatch, err
+		return obiiter.NilIBioSequence, err
 	}
 
-	reverse, err := obiconvert.ReadBioSequences(_ReverseFiles...)
+	reverse, err := obiconvert.CLIReadBioSequences(_ReverseFile)
 	if err != nil {
-		return obiiter.NilIPairedBioSequenceBatch, err
+		return obiiter.NilIBioSequence, err
 	}
 
-	paired := forward.PairWith(reverse)
+	paired := forward.PairTo(reverse)
 
 	return paired, nil
 }
 
-func Delta() int {
+func CLIDelta() int {
 	return _Delta
 }
 
-func MinOverlap() int {
+func CLIMinOverlap() int {
 	return _MinOverlap
 }
 
-func MinIdentity() float64 {
+func CLIMinIdentity() float64 {
 	return _MinIdentity
 }
 
-func GapPenality() float64 {
+func CLIGapPenality() float64 {
 	return _GapPenality
 }
 
-func WithStats() bool {
+func CLIWithStats() bool {
 	return !_WithoutStats
 }

pkg/obitools/obipairing/pairing.go

@@ -3,12 +3,12 @@ package obipairing
 import (
 	"math"
 	"os"
-	"runtime"
 
 	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 	"github.com/schollz/progressbar/v3"
 )
@@ -203,12 +203,16 @@ func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
 //
 // The function returns an iterator over batches of obiseq.Biosequence object.
 // each pair of processed sequences produces one sequence in the result iterator.
-func IAssemblePESequencesBatch(iterator obiiter.IPairedBioSequenceBatch,
+func IAssemblePESequencesBatch(iterator obiiter.IBioSequence,
 	gap float64, delta, minOverlap int,
 	minIdentity float64,
 	withStats bool, sizes ...int) obiiter.IBioSequence {
 
-	nworkers := runtime.NumCPU() * 3 / 2
+	if !iterator.IsPaired() {
+		log.Fatalln("Sequence data must be paired")
+	}
+
+	nworkers := obioptions.CLIMaxCPU() * 3 / 2
 	buffsize := iterator.BufferSize()
 
 	if len(sizes) > 0 {
@@ -236,15 +240,15 @@ func IAssemblePESequencesBatch(iterator obiiter.IPairedBioSequenceBatch,
 		progressbar.OptionShowIts(),
 		progressbar.OptionSetDescription("[Sequence Pairing]"))
 
-	f := func(iterator obiiter.IPairedBioSequenceBatch, wid int) {
+	f := func(iterator obiiter.IBioSequence, wid int) {
 		arena := obialign.MakePEAlignArena(150, 150)
 
 		for iterator.Next() {
 			batch := iterator.Get()
-			cons := make(obiseq.BioSequenceSlice, len(batch.Forward()))
+			cons := make(obiseq.BioSequenceSlice, len(batch.Slice()))
 			processed := 0
-			for i, A := range batch.Forward() {
-				B := batch.Reverse()[i]
+			for i, A := range batch.Slice() {
+				B := A.PairedWith()
 				cons[i] = AssemblePESequences(A, B, gap, delta, minOverlap, minIdentity, withStats, true, arena)
 				if i%59 == 0 {
 					bar.Add(59)