First version of obimatrix

Former-commit-id: 6e09eb0dd75bc688a6c83ef40dd88658fb1b296e

cmd/obitools/obimatrix/main.go

@@ -0,0 +1,56 @@
+package main
+
+import (
+	"fmt"
+	"os"
+
+	log "github.com/sirupsen/logrus"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obimatrix"
+)
+
+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(
+		obimatrix.OptionSet,
+	)
+
+	_, args := optionParser(os.Args)
+
+	fs, err := obiconvert.CLIReadBioSequences(args...)
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)", err)
+		os.Exit(1)
+	}
+
+	matrix := obimatrix.IMatrix(fs)
+
+	if obimatrix.CLIOutFormat() == "matrix" {
+		obimatrix.CLIWriteCSVToStdout(matrix)
+	} else {
+		obimatrix.CLIWriteThreeColumnsToStdout(matrix)
+	}
+	fmt.Printf("\n")
+}

cmd/obitools/obisummary/main.go

@@ -34,10 +34,7 @@ func main() {
 	// trace.Start(ftrace)
 	// defer trace.Stop()
 
-	optionParser := obioptions.GenerateOptionParser(
-		obiconvert.InputOptionSet,
-		obisummary.OptionSet,
-	)
+	optionParser := obioptions.GenerateOptionParser(obisummary.OptionSet)
 
 	_, args := optionParser(os.Args)