Work on iterators and recycling of biosequences

cmd/obitools/obiconvert/main.go

@@ -13,6 +13,6 @@ func main() {
 
 	_, args, _ := optionParser(os.Args)
 
-	fs, _ := obiconvert.ReadBioSequences(args...)
-	obiconvert.WriteBioSequences(fs)
+	fs, _ := obiconvert.ReadBioSequencesBatch(args...)
+	obiconvert.WriteBioSequencesBatch(fs,true)
 }

cmd/obitools/obicount/main.go

@@ -4,7 +4,6 @@ import (
 	"fmt"
 	"log"
 	"os"
-	"runtime/trace"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obicount"
@@ -21,12 +20,12 @@ func main() {
 	// pprof.StartCPUProfile(f)
 	// defer pprof.StopCPUProfile()
 
-	ftrace, err := os.Create("cpu.trace")
-	if err != nil {
-		log.Fatal(err)
-	}
-	trace.Start(ftrace)
-	defer trace.Stop()
+	// ftrace, err := os.Create("cpu.trace")
+	// if err != nil {
+	// 	log.Fatal(err)
+	// }
+	// trace.Start(ftrace)
+	// defer trace.Stop()
 
 	optionParser := obioptions.GenerateOptionParser(
 		obiconvert.InputOptionSet,
@@ -47,6 +46,7 @@ func main() {
 		nread += s.Count()
 		nvariant++
 		nsymbol += s.Length()
+		(&s).Recycle()
 	}
 
 	if obicount.IsPrintingVariantCount() {

cmd/obitools/obipairing/main.go

@@ -1,24 +1,22 @@
 package main
 
 import (
-	"log"
 	"os"
-	"runtime/pprof"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
 	"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/obipairing"
 )
 
 func main() {
 
 	// go tool pprof -http=":8000" ./obipairing ./cpu.pprof
-	f, err := os.Create("cpu.pprof")
-	if err != nil {
-		log.Fatal(err)
-	}
-	pprof.StartCPUProfile(f)
-	defer pprof.StopCPUProfile()
+	// f, err := os.Create("cpu.pprof")
+	// if err != nil {
+	// 	log.Fatal(err)
+	// }
+	// pprof.StartCPUProfile(f)
+	// defer pprof.StopCPUProfile()
 
 	// go tool trace cpu.trace
 	// ftrace, err := os.Create("cpu.trace")
@@ -33,6 +31,5 @@ func main() {
 	optionParser(os.Args)
 	pairs, _ := obipairing.IBatchPairedSequence()
 	paired := obipairing.IAssemblePESequencesBatch(pairs, 2, 50, 20, true)
-	written, _ := obiformats.WriteFastqBatchToStdout(paired)
-	written.Destroy()
+	obiconvert.WriteBioSequencesBatch(paired, true)
 }

cmd/obitools/obipcr/main.go

@@ -30,5 +30,5 @@ func main() {
 
 	sequences, _ := obiconvert.ReadBioSequencesBatch(args...)
 	amplicons, _ := obipcr.PCR(sequences)
-	obiconvert.WriteBioSequences(amplicons)
+	obiconvert.WriteBioSequencesBatch(amplicons,true)
 }

cmd/test/main.go

@@ -59,4 +59,9 @@ func main() {
 	sA.ReverseComplement(true)
 	fmt.Println(string(sA.Sequence()))
 	fmt.Println(string(sA.Id()))
+
+	sA.Reset()
+	fmt.Println(sA.Length())
+	fmt.Println(sA.String())
+
 }