Add a new command obitagpcr able to tag reads according to their corresponding pcr samples

Former-commit-id: 1f34bf0a27d55afc3556efd64f6ccee6d2329aff

cmd/obitools/obitagpcr/main.go

@@ -0,0 +1,55 @@
+package main
+
+import (
+	"os"
+
+	log "github.com/sirupsen/logrus"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
+	"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"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obitagpcr"
+)
+
+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()
+
+	obioptions.SetWorkerPerCore(1)
+
+	optionParser := obioptions.GenerateOptionParser(obitagpcr.OptionSet)
+
+	optionParser(os.Args)
+	pairs, err := obipairing.CLIPairedSequence()
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)", err)
+		os.Exit(1)
+	}
+
+	paired := obitagpcr.IPCRTagPESequencesBatch(pairs,
+		obipairing.CLIGapPenality(),
+		obipairing.CLIDelta(),
+		obipairing.CLIMinOverlap(),
+		obipairing.CLIMinIdentity(),
+		obipairing.CLIWithStats())
+
+	obiconvert.CLIWriteBioSequences(paired, true)
+
+	obiiter.WaitForLastPipe()
+}