Adds the reading of the options through the csv formated ngsfilter configuration file

Former-commit-id: 0e9a13689da2ba45293c7de1f728d3d0d34d3238

pkg/obiformats/ngsfilter_read.go

@@ -226,7 +226,7 @@ func ReadOldNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
 }
 
 var library_parameter = map[string]func(library *obingslibrary.NGSLibrary, values ...string){
-	"@spacer": func(library *obingslibrary.NGSLibrary, values ...string) {
+	"spacer": func(library *obingslibrary.NGSLibrary, values ...string) {
 		switch len(values) {
 		case 0:
 			log.Fatalln("Missing value for @spacer parameter")
@@ -251,6 +251,108 @@ var library_parameter = map[string]func(library *obingslibrary.NGSLibrary, value
 			log.Fatalln("Invalid value for @spacer parameter")
 		}
 	},
+	"forward_spacer": func(library *obingslibrary.NGSLibrary, values ...string) {
+		switch len(values) {
+		case 0:
+			log.Fatalln("Missing value for @forward_spacer parameter")
+		case 1:
+			spacer, err := strconv.Atoi(values[0])
+
+			if err != nil {
+				log.Fatalln("Invalid value for @forward_spacer parameter")
+			}
+
+			library.SetForwardTagSpacer(spacer)
+		default:
+			log.Fatalln("Invalid value for @forward_spacer parameter")
+		}
+	},
+	"reverse_spacer": func(library *obingslibrary.NGSLibrary, values ...string) {
+		switch len(values) {
+		case 0:
+			log.Fatalln("Missing value for @reverse_spacer parameter")
+		case 1:
+			spacer, err := strconv.Atoi(values[0])
+
+			if err != nil {
+				log.Fatalln("Invalid value for @reverse_spacer parameter")
+			}
+
+			library.SetReverseTagSpacer(spacer)
+		default:
+			log.Fatalln("Invalid value for @reverse_spacer parameter")
+		}
+	},
+	"tag_delimiter": func(library *obingslibrary.NGSLibrary, values ...string) {
+		switch len(values) {
+		case 0:
+			log.Fatalln("Missing value for @tag_delimiter parameter")
+		case 1:
+			library.SetTagDelimiter([]byte(values[0])[0])
+		case 2:
+			library.SetTagDelimiterFor(values[0], []byte(values[1])[0])
+		default:
+			log.Fatalln("Invalid value for @tag_delimiter parameter")
+		}
+	},
+	"forward_tag_delimiter": func(library *obingslibrary.NGSLibrary, values ...string) {
+		switch len(values) {
+		case 0:
+			log.Fatalln("Missing value for @forward_tag_delimiter parameter")
+		case 1:
+			library.SetForwardTagDelimiter([]byte(values[0])[0])
+		default:
+			log.Fatalln("Invalid value for @forward_tag_delimiter parameter")
+		}
+	},
+	"reverse_tag_delimiter": func(library *obingslibrary.NGSLibrary, values ...string) {
+		switch len(values) {
+		case 0:
+			log.Fatalln("Missing value for @reverse_tag_delimiter parameter")
+		case 1:
+			library.SetReverseTagDelimiter([]byte(values[0])[0])
+		default:
+			log.Fatalln("Invalid value for @reverse_tag_delimiter parameter")
+		}
+	},
+	"matching": func(library *obingslibrary.NGSLibrary, values ...string) {
+		switch len(values) {
+		case 0:
+			log.Fatalln("Missing value for @matching parameter")
+		case 1:
+			if err := library.SetMatching(values[0]); err != nil {
+				log.Fatalf("Invalid value %s for @matching parameter", values[0])
+			}
+		default:
+			log.Fatalln("Invalid value for @matching parameter")
+		}
+	},
+	"primer_mismatches": func(library *obingslibrary.NGSLibrary, values ...string) {
+		switch len(values) {
+		case 0:
+			log.Fatalln("Missing value for @primer_error parameter")
+		case 1:
+			dist, err := strconv.Atoi(values[0])
+
+			if err != nil {
+				log.Fatalf("Invalid value %s for @primer_error parameter", values[0])
+			}
+
+			library.SetAllowedMismatch(dist)
+		default:
+			log.Fatalln("Invalid value for @primer_error parameter")
+		}
+	},
+	"indels": func(library *obingslibrary.NGSLibrary, values ...string) {
+		switch len(values) {
+		case 0:
+			log.Fatalln("Missing value for @indels parameter")
+		case 1:
+			library.SetAllowsIndels(values[0] == "true")
+		default:
+			log.Fatalln("Invalid value for @indels parameter")
+		}
+	},
 }
 
 func ReadCSVNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
@@ -272,20 +374,9 @@ func ReadCSVNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
 
 	i := 0
 	for i = 0; i < len(records) && records[i][0] == "@param"; i++ {
-		param := records[i][1]
-		if len(records[i]) < 3 {
-			log.Fatalf("At line %d: Missing value for parameter %s", i, param)
-		}
-		data := records[i][2:]
-		setparam, ok := library_parameter[param]
-
-		if ok {
-			setparam(&ngsfilter, data...)
-		} else {
-			log.Warnf("At line %d: Skipping unknown parameter %s: %v", i, param, data)
-		}
 	}
 
+	params := records[0:i]
 	records = records[i:]
 
 	header := records[0]
@@ -371,5 +462,20 @@ func ReadCSVNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
 
 	}
 
+	for i := 0; i < len(params); i++ {
+		param := params[i][1]
+		if len(params[i]) < 3 {
+			log.Fatalf("At line %d: Missing value for parameter %s", i, param)
+		}
+		data := params[i][2:]
+		setparam, ok := library_parameter[param]
+
+		if ok {
+			setparam(&ngsfilter, data...)
+		} else {
+			log.Warnf("At line %d: Skipping unknown parameter %s: %v", i, param, data)
+		}
+	}
+
 	return &ngsfilter, nil
 }

pkg/obingslibrary/ngslibrary.go

@@ -24,15 +24,20 @@ type PCR struct {
 }
 
 type NGSLibrary struct {
-	Matching string
+	Matching           string
-	Primers  map[string]PrimerPair
+	Allowed_mismatches int
-	Markers  map[PrimerPair]*Marker
+	Allows_indels      bool
+	Primers            map[string]PrimerPair
+	Markers            map[PrimerPair]*Marker
 }
 
 func MakeNGSLibrary() NGSLibrary {
 	return NGSLibrary{
-		Primers: make(map[string]PrimerPair, 10),
+		Matching:           "strict",
-		Markers: make(map[PrimerPair]*Marker, 10),
+		Allowed_mismatches: 2,
+		Allows_indels:      false,
+		Primers:            make(map[string]PrimerPair, 10),
+		Markers:            make(map[PrimerPair]*Marker, 10),
 	}
 }
 
@@ -109,6 +114,22 @@ func (library *NGSLibrary) SetTagDelimiter(delim byte) {
 	library.SetReverseTagDelimiter(delim)
 }
 
+func (library *NGSLibrary) SetTagDelimiterFor(primer string, delim byte) {
+	primers, ok := library.Primers[primer]
+
+	if ok {
+		marker, ok := library.Markers[primers]
+
+		if ok {
+			if primer == primers.Forward {
+				marker.SetForwardTagDelimiter(delim)
+			} else {
+				marker.SetReverseTagDelimiter(delim)
+			}
+		}
+	}
+}
+
 func (library *NGSLibrary) CheckTagLength() {
 
 	for _, marker := range library.Markers {
@@ -132,3 +153,28 @@ func (library *NGSLibrary) CheckPrimerUnicity() error {
 	}
 	return nil
 }
+
+// SetMatching sets the matching strategy for the library.
+// Returns an error if the matching strategy is invalid.
+func (library *NGSLibrary) SetMatching(matching string) error {
+	switch matching {
+	case "strict", "hamming", "indel": // Valid matching strategies
+		library.Matching = matching
+	default:
+		return fmt.Errorf("invalid matching : %s", matching)
+	}
+	return nil
+}
+
+func (library *NGSLibrary) SetAllowedMismatch(allowed_mismatches int) {
+	if allowed_mismatches < 0 {
+		allowed_mismatches = 0
+	}
+	library.Allowed_mismatches = allowed_mismatches
+}
+
+// SetAllowsIndels sets whether the library allows indels.
+// The value of the argument allows_indels is directly assigned to the library's Allows_indels field.
+func (library *NGSLibrary) SetAllowsIndels(allows_indels bool) {
+	library.Allows_indels = allows_indels
+}

pkg/obioptions/version.go

@@ -7,7 +7,7 @@ import (
 // TODO: The version number is extracted from git. This induces that the version
 // corresponds to the last commit, and not the one when the file will be
 // commited
-var _Commit = "d00f335"
+var _Commit = "5affee2"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.