Correct for a strange bug...

cmd/obitools/obipairing/main.go

@@ -7,7 +7,6 @@ import (
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obimultiplex"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obipairing"
 )
 
@@ -29,7 +28,7 @@ func main() {
 	trace.Start(ftrace)
 	defer trace.Stop()
 
-	optionParser := obioptions.GenerateOptionParser(obimultiplex.OptionSet)
+	optionParser := obioptions.GenerateOptionParser(obipairing.OptionSet)
 
 	optionParser(os.Args)
 	pairs, _ := obipairing.IBatchPairedSequence()

pkg/obiformats/binary_write.go

@@ -0,0 +1,153 @@
+package obiformats
+
+import (
+	"io"
+	"log"
+	"os"
+	"time"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"github.com/renproject/surge"
+)
+
+func WriteBinary(iterator obiseq.IBioSequence, file io.Writer) error {
+	singleseq := make(obiseq.BioSequenceSlice, 1)
+	blob := make([]byte, 0, 1024)
+	for iterator.Next() {
+		singleseq[0] = iterator.Get()
+		blobsize := singleseq.SizeHint()
+		if blobsize > cap(blob) {
+			blob = make([]byte, 0, blobsize*2+8)
+		}
+		_, _, err := surge.MarshalI64(int64(blobsize), blob, 8)
+		if err != nil {
+			return err
+		}
+		data := blob[8 : 8+blobsize]
+		_, _, err = singleseq.Marshal(data, blobsize)
+		if err != nil {
+			return err
+		}
+
+		file.Write(blob[0 : 8+blobsize])
+	}
+
+	return nil
+}
+
+func WriteBinaryToFile(iterator obiseq.IBioSequence,
+	filename string) error {
+
+	file, err := os.Create(filename)
+
+	if err != nil {
+		log.Fatalf("open file error: %v", err)
+		return err
+	}
+
+	return WriteBinary(iterator, file)
+}
+
+func WriteBinaryToStdout(iterator obiseq.IBioSequence) error {
+	return WriteBinary(iterator, os.Stdout)
+}
+
+func WriteBinaryBatch(iterator obiseq.IBioSequenceBatch, file io.Writer, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
+	opt := MakeOptions(options)
+
+	buffsize := iterator.BufferSize()
+	newIter := obiseq.MakeIBioSequenceBatch(buffsize)
+
+	nwriters := opt.ParallelWorkers()
+
+	chunkchan := make(chan FileChunck)
+
+	newIter.Add(nwriters)
+
+	go func() {
+		newIter.Wait()
+		for len(chunkchan) > 0 {
+			time.Sleep(time.Millisecond)
+		}
+		close(chunkchan)
+		for len(newIter.Channel()) > 0 {
+			time.Sleep(time.Millisecond)
+		}
+		close(newIter.Channel())
+	}()
+
+	ff := func(iterator obiseq.IBioSequenceBatch) {
+		blob := make([]byte, 0, 10240)
+		for iterator.Next() {
+			batch := iterator.Get()
+			blobsize := batch.Slice().SizeHint()
+			if blobsize > cap(blob) {
+				blob = make([]byte, 0, blobsize*2+8)
+			}
+			_, _, err := surge.MarshalI64(int64(blobsize), blob, 8)
+			if err != nil {
+				log.Fatalf("error in reading binary file %v\n", err)
+			}
+			data := blob[8 : 8+blobsize]
+			_, _, err = batch.Slice().Marshal(data, blobsize)
+			if err != nil {
+				log.Fatalf("error in reading binary file %v\n", err)
+			}
+
+			chunkchan <- FileChunck{
+				data,
+				batch.Order(),
+			}
+			newIter.Channel() <- batch
+		}
+		newIter.Done()
+	}
+
+	log.Println("Start of the binary file writing")
+	go ff(iterator)
+	for i := 0; i < nwriters-1; i++ {
+		go ff(iterator.Split())
+	}
+
+	next_to_send := 0
+	received := make(map[int]FileChunck, 100)
+
+	go func() {
+		for chunk := range chunkchan {
+			if chunk.order == next_to_send {
+				file.Write(chunk.text)
+				next_to_send++
+				chunk, ok := received[next_to_send]
+				for ok {
+					file.Write(chunk.text)
+					delete(received, next_to_send)
+					next_to_send++
+					chunk, ok = received[next_to_send]
+				}
+			} else {
+				received[chunk.order] = chunk
+			}
+
+		}
+	}()
+
+	return newIter, nil
+}
+
+func WriteBinaryBatchToStdout(iterator obiseq.IBioSequenceBatch, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
+	return WriteBinaryBatch(iterator, os.Stdout, options...)
+}
+
+func WriteBinaryBatchToFile(iterator obiseq.IBioSequenceBatch,
+	filename string,
+	options ...WithOption) (obiseq.IBioSequenceBatch, error) {
+
+	file, err := os.Create(filename)
+
+	if err != nil {
+		log.Fatalf("open file error: %v", err)
+		return obiseq.NilIBioSequenceBatch, err
+	}
+
+	return WriteBinaryBatch(iterator, file, options...)
+}

pkg/obingslibrary/worker.go

@@ -143,11 +143,11 @@ func MakeOptions(setters []WithOption) Options {
 func _ExtractBarcodeSlice(ngslibrary NGSLibrary,
 	sequences obiseq.BioSequenceSlice,
 	options Options) obiseq.BioSequenceSlice {
-	newSlice := make(obiseq.BioSequenceSlice,0,len(sequences))
+	newSlice := make(obiseq.BioSequenceSlice, 0, len(sequences))
-	
+
 	for _, seq := range sequences {
-		s, err := ngslibrary.ExtractBarcode(seq,true)
+		s, err := ngslibrary.ExtractBarcode(seq, true)
-		if err==nil || ! options.pointer.discardErrors {
+		if err == nil || !options.pointer.discardErrors {
 			newSlice = append(newSlice, s)
 		}
 	}
@@ -179,4 +179,3 @@ func ExtractBarcodeSliceWorker(ngslibrary NGSLibrary,
 
 	return worker
 }
-

pkg/obioptions/options.go

@@ -27,7 +27,6 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 		options.Description("Number of parallele threads computing the result"))
 
 	options.IntVar(&_MaxAllowedCPU, "max-cpu", _MaxAllowedCPU,
-		options.Alias("w"),
 		options.Description("Number of parallele threads computing the result"))
 
 	for _, o := range optionset {

pkg/obitools/obipairing/options.go

@@ -30,7 +30,7 @@ func PairingOptionSet(options *getoptions.GetOpt) {
 		options.Alias("O"),
 		options.Description("Minimum ovelap between both the reads to consider the aligment"))
 	options.Float64Var(&_MinIdentity, "min-identity", _MinIdentity,
-		options.Alias("O"),
+		options.Alias("X"),
 		options.Description("Minimum identity between ovelaped regions of the reads to consider the aligment"))
 	options.Float64Var(&_GapPenality, "gap-penality", _GapPenality,
 		options.Alias("G"),

pkg/obitools/obipairing/pairing.go

@@ -105,7 +105,7 @@ func JoinPairedSequence(seqA, seqB obiseq.BioSequence, inplace bool) obiseq.BioS
 // input sequence.
 //
 func AssemblePESequences(seqA, seqB obiseq.BioSequence,
-	gap float64, delta, minOverlap int, minIdentity float64,withStats bool,
+	gap float64, delta, minOverlap int, minIdentity float64, withStats bool,
 	inplace bool,
 	arenaAlign obialign.PEAlignArena) obiseq.BioSequence {
 
@@ -119,7 +119,7 @@ func AssemblePESequences(seqA, seqB obiseq.BioSequence,
 	}
 	lcons := cons.Length()
 	aliLength := lcons - _Abs(left) - _Abs(right)
-	identity := float64(match)/float64(aliLength)
+	identity := float64(match) / float64(aliLength)
 
 	if aliLength >= minOverlap && identity >= minIdentity {
 		if withStats {
@@ -268,7 +268,6 @@ func IAssemblePESequencesBatch(iterator obiseq.IPairedBioSequenceBatch,
 		go f(iterator.Split(), i)
 	}
 	go f(iterator, nworkers-1)
-
 	return newIter
 
 }

pkg/obitools/obipcr/pcr.go

@@ -14,11 +14,11 @@ func PCR(iterator obiseq.IBioSequenceBatch) (obiseq.IBioSequenceBatch, error) {
 
 	opts = append(opts,
 		obiapat.OptionForwardPrimer(
-			ForwardPrimer(), 
+			ForwardPrimer(),
 			AllowedMismatch(),
 		),
 		obiapat.OptionReversePrimer(
-			ReversePrimer(), 
+			ReversePrimer(),
 			AllowedMismatch(),
 		),
 	)