Patch a bug on writing to stdout, and add clearer error on openning data files

cmd/obitools/obikmersimcount/main.go

@@ -0,0 +1,58 @@
+package main
+
+import (
+	"log"
+	"os"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obikmersim"
+)
+
+func main() {
+
+	defer obiseq.LogBioSeqStatus()
+
+	// 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()
+
+	optionParser := obioptions.GenerateOptionParser(obikmersim.CountOptionSet)
+
+	_, args := optionParser(os.Args)
+
+	var err error
+	sequences := obiiter.NilIBioSequence
+
+	if !obikmersim.CLISelf() {
+		sequences, err = obiconvert.CLIReadBioSequences(args...)
+	}
+
+	obiconvert.OpenSequenceDataErrorMessage(args, err)
+
+	selected := obikmersim.CLILookForSharedKmers(sequences)
+	topull, err := obiconvert.CLIWriteBioSequences(selected, false)
+
+	if err == nil {
+		log.Panic(err)
+	}
+
+	topull.Consume()
+
+	obiiter.WaitForLastPipe()
+
+}