First commit

cmd/obitools/obipairing/main.go

@@ -0,0 +1,38 @@
+package main
+
+import (
+	"log"
+	"os"
+	"runtime/pprof"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiformats"
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obioptions"
+	"git.metabarcoding.org/lecasofts/go/oa2/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()
+
+	// go tool trace cpu.trace
+	// ftrace, err := os.Create("cpu.trace")
+	// if err != nil {
+	// 	log.Fatal(err)
+	// }
+	// trace.Start(ftrace)
+	// defer trace.Stop()
+
+	option_parser := obioptions.GenerateOptionParser(obipairing.OptionSet)
+
+	option_parser(os.Args)
+	pairs, _ := obipairing.IBatchPairedSequence()
+	paired := obipairing.IAssemblePESequencesBatch(pairs, 2, 50, 20, true)
+	written, _ := obiformats.WriteFastqBatchToStdout(paired)
+	written.Destroy()
+}