first version of obidemerge, obijoin and a new filter for obicleandb but to be finnished

Former-commit-id: 8a1ed26e5548c30db75644c294d478ec4d753f19

pkg/obitools/obijoin/options.go

@@ -0,0 +1,90 @@
+package obijoin
+
+import (
+	"strings"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
+	"github.com/DavidGamba/go-getoptions"
+)
+
+var _by = []string{}
+var _join = ""
+var _UpdateID = false
+var _UpdateSequence = false
+var _UpdateQuality = false
+
+type By struct {
+	Left  []string
+	Right []string
+}
+
+func JoinOptionSet(options *getoptions.GetOpt) {
+
+	options.StringSliceVar(&_by, "by", 1, 1,
+		options.Alias("b"),
+		options.Description("to declare join keys."))
+
+	options.StringVar(&_join, "join-with", _join,
+		options.Alias("j"),
+		options.Description("file name of the file to join with."),
+		options.Required("You must provide a file name to join with."))
+
+	options.BoolVar(&_UpdateID, "update-id", _UpdateID,
+		options.Alias("i"),
+		options.Description("Update the sequence IDs in the joined file."))
+
+	options.BoolVar(&_UpdateSequence, "update-sequence", _UpdateSequence,
+		options.Alias("s"),
+		options.Description("Update the sequence in the joined file."))
+
+	options.BoolVar(&_UpdateQuality, "update-quality", _UpdateQuality,
+		options.Alias("q"),
+		options.Description("Update the quality in the joined file."))
+
+}
+
+// OptionSet adds to the basic option set every options declared for
+// the obipcr command
+func OptionSet(options *getoptions.GetOpt) {
+	obiconvert.OptionSet(options)
+	JoinOptionSet(options)
+}
+
+func CLIBy() By {
+	if len(_by) == 0 {
+		return By{
+			Left:  []string{"id"},
+			Right: []string{"id"},
+		}
+	}
+
+	left := make([]string, len(_by))
+	right := make([]string, len(_by))
+
+	for i, v := range _by {
+		vals := strings.Split(v, "=")
+		left[i] = vals[0]
+		right[i] = vals[0]
+		if len(vals) > 1 {
+			right[i] = vals[1]
+		}
+	}
+
+	return By{Left: left, Right: right}
+}
+
+func CLIJoinWith() string {
+	return _join
+}
+
+func CLIUpdateId() bool {
+	return _UpdateID
+}
+
+func CLIUpdateSequence() bool {
+	return _UpdateSequence
+}
+
+func CLIUpdateQuality() bool {
+	return _UpdateQuality
+}