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

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)