Patch the production of the ratio file

README.md

@@ -37,7 +37,7 @@ curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install
       bash -s -- --install-dir test_install --obitools-prefix k
 ```
 
-In this case, the binaries will be installed in the `test_install` directory and all command names will be prefixed with the letter `k`. Thus `obigrep` will be named `kobigrep`.
+In this case, the binaries will be installed in the `test_install` directory and all command names will be prefixed with the letter `k`. Thus, `obigrep` will be named `kobigrep`.
 
 ## Continuing the analysis...
 

pkg/obiformats/fastseq_json_header.go

@@ -13,7 +13,7 @@ import (
 	"github.com/buger/jsonparser"
 )
 
-func _parse_json_map_string(str []byte, sequence *obiseq.BioSequence) (map[string]string, error) {
+func _parse_json_map_string(str []byte) (map[string]string, error) {
 	values := make(map[string]string)
 	jsonparser.ObjectEach(str,
 		func(key []byte, value []byte, dataType jsonparser.ValueType, offset int) (err error) {
@@ -25,7 +25,7 @@ func _parse_json_map_string(str []byte, sequence *obiseq.BioSequence) (map[strin
 	return values, nil
 }
 
-func _parse_json_map_int(str []byte, sequence *obiseq.BioSequence) (map[string]int, error) {
+func _parse_json_map_int(str []byte) (map[string]int, error) {
 	values := make(map[string]int)
 	jsonparser.ObjectEach(str,
 		func(key []byte, value []byte, dataType jsonparser.ValueType, offset int) (err error) {
@@ -41,7 +41,7 @@ func _parse_json_map_int(str []byte, sequence *obiseq.BioSequence) (map[string]i
 	return values, nil
 }
 
-func _parse_json_map_float(str []byte, sequence *obiseq.BioSequence) (map[string]float64, error) {
+func _parse_json_map_float(str []byte) (map[string]float64, error) {
 	values := make(map[string]float64)
 	jsonparser.ObjectEach(str,
 		func(key []byte, value []byte, dataType jsonparser.ValueType, offset int) (err error) {
@@ -57,7 +57,7 @@ func _parse_json_map_float(str []byte, sequence *obiseq.BioSequence) (map[string
 	return values, nil
 }
 
-func _parse_json_map_bool(str []byte, sequence *obiseq.BioSequence) (map[string]bool, error) {
+func _parse_json_map_bool(str []byte) (map[string]bool, error) {
 	values := make(map[string]bool)
 	jsonparser.ObjectEach(str,
 		func(key []byte, value []byte, dataType jsonparser.ValueType, offset int) (err error) {
@@ -73,7 +73,7 @@ func _parse_json_map_bool(str []byte, sequence *obiseq.BioSequence) (map[string]
 	return values, nil
 }
 
-func _parse_json_map_interface(str []byte, sequence *obiseq.BioSequence) (map[string]interface{}, error) {
+func _parse_json_map_interface(str []byte) (map[string]interface{}, error) {
 	values := make(map[string]interface{})
 	jsonparser.ObjectEach(str,
 		func(key []byte, value []byte, dataType jsonparser.ValueType, offset int) (err error) {
@@ -100,7 +100,7 @@ func _parse_json_map_interface(str []byte, sequence *obiseq.BioSequence) (map[st
 	return values, nil
 }
 
-func _parse_json_array_string(str []byte, sequence *obiseq.BioSequence) ([]string, error) {
+func _parse_json_array_string(str []byte) ([]string, error) {
 	values := make([]string, 0)
 	jsonparser.ArrayEach(str,
 		func(value []byte, dataType jsonparser.ValueType, offset int, err error) {
@@ -162,7 +162,7 @@ func _parse_json_array_bool(str []byte, sequence *obiseq.BioSequence) ([]bool, e
 	return values, nil
 }
 
-func _parse_json_array_interface(str []byte, sequence *obiseq.BioSequence) ([]interface{}, error) {
+func _parse_json_array_interface(str []byte) ([]interface{}, error) {
 	values := make([]interface{}, 0)
 	jsonparser.ArrayEach(str,
 		func(value []byte, dataType jsonparser.ValueType, offset int, err error) {
@@ -261,14 +261,14 @@ func _parse_json_header_(header string, sequence *obiseq.BioSequence) string {
 				sequence.SetCount(int(count))
 
 			case skey == "obiclean_weight":
-				weight, err := _parse_json_map_int(value, sequence)
+				weight, err := _parse_json_map_int(value)
 				if err != nil {
 					log.Fatalf("%s: Cannot parse obiclean weight %s", sequence.Id(), string(value))
 				}
 				annotations[skey] = weight
 
 			case skey == "obiclean_status":
-				status, err := _parse_json_map_string(value, sequence)
+				status, err := _parse_json_map_string(value)
 				if err != nil {
 					log.Fatalf("%s: Cannot parse obiclean status %s", sequence.Id(), string(value))
 				}
@@ -276,7 +276,7 @@ func _parse_json_header_(header string, sequence *obiseq.BioSequence) string {
 
 			case strings.HasPrefix(skey, "merged_"):
 				if dataType == jsonparser.Object {
-					data, err := _parse_json_map_int(value, sequence)
+					data, err := _parse_json_map_int(value)
 					if err != nil {
 						log.Fatalf("%s: Cannot parse merged slot %s: %v", sequence.Id(), skey, err)
 					} else {
@@ -316,9 +316,9 @@ func _parse_json_header_(header string, sequence *obiseq.BioSequence) string {
 						annotations[skey], err = strconv.ParseFloat(obiutils.UnsafeString(value), 64)
 					}
 				case jsonparser.Array:
-					annotations[skey], err = _parse_json_array_interface(value, sequence)
+					annotations[skey], err = _parse_json_array_interface(value)
 				case jsonparser.Object:
-					annotations[skey], err = _parse_json_map_interface(value, sequence)
+					annotations[skey], err = _parse_json_map_interface(value)
 				case jsonparser.Boolean:
 					annotations[skey], err = jsonparser.ParseBoolean(value)
 				case jsonparser.Null:

pkg/obioptions/version.go

@@ -8,7 +8,7 @@ import (
 // corresponds to the last commit, and not the one when the file will be
 // commited
 
-var _Commit = "6245d7f"
+var _Commit = "791d253"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.

pkg/obitools/obiclean/graph.go

@@ -20,11 +20,11 @@ import (
 type Ratio struct {
 	Sample         string
 	SeqID          string
-	status string
+	OriginalStatus string
-	From   int
+	WOriginal      int
-	To     int
+	WMutant        int
-	CFrom  int
+	COriginal      int
-	CTo    int
+	CMutant        int
 	Pos            int
 	Length         int
 	A              int
@@ -59,13 +59,15 @@ func makeEdge(father, dist, pos int, from, to byte) Edge {
 // ratio
 func EmpiricalDistCsv(filename string, data [][]Ratio, compressed bool) {
 	file, err := os.Create(filename)
-
+	if err != nil {
-	defer file.Close()
+		fmt.Println(err)
+	}
 
 	destfile, err := obiutils.CompressStream(file, true, true)
 	if err != nil {
 		fmt.Println(err)
 	}
+	defer destfile.Close()
 
 	pbopt := make([]progressbar.Option, 0, 5)
 	pbopt = append(pbopt,
@@ -78,19 +80,19 @@ func EmpiricalDistCsv(filename string, data [][]Ratio, compressed bool) {
 
 	bar := progressbar.NewOptions(len(data), pbopt...)
 
-	fmt.Fprintln(destfile, "Sample,Father_id,Father_status,From,To,Weight_from,Weight_to,Count_from,Count_to,Position,length,A,C,G,T")
+	fmt.Fprintln(destfile, "Sample,Origin_id,Origin_status,Origin,Mutant,Origin_Weight,Mutant_Weight,Origin_Count,Mutant_Count,Position,Origin_length,A,C,G,T")
 	for code, dist := range data {
 		a1, a2 := intToNucPair(code)
 		for _, ratio := range dist {
 			fmt.Fprintf(destfile, "%s,%s,%s,%c,%c,%d,%d,%d,%d,%d,%d,%d,%d,%d,%d\n",
 				ratio.Sample,
 				ratio.SeqID,
-				ratio.status,
+				ratio.OriginalStatus,
 				a1, a2,
-				ratio.From,
+				ratio.WOriginal,
-				ratio.To,
+				ratio.WMutant,
-				ratio.CFrom,
+				ratio.COriginal,
-				ratio.CTo,
+				ratio.CMutant,
 				ratio.Pos,
 				ratio.Length,
 				ratio.A,
@@ -453,16 +455,20 @@ func EstimateRatio(samples map[string]*[]*seqPCR, minStatRatio int) [][]Ratio {
 				if father.Weight >= minStatRatio && edge.Dist == 1 {
 					s := father.Sequence.Sequence()
 					ratio[edge.NucPair] = append(ratio[edge.NucPair],
-						Ratio{name,
+						Ratio{
-							father.Sequence.Id(), Status(father.Sequence)[name],
+							Sample:         name,
-							father.Weight, seq.Weight,
+							SeqID:          father.Sequence.Id(),
-							father.Count, seq.Count,
+							OriginalStatus: Status(father.Sequence)[name],
-							edge.Pos,
+							WOriginal:      father.Weight,
-							father.Sequence.Len(),
+							WMutant:        seq.Weight,
-							bytes.Count(s, []byte("a")),
+							COriginal:      father.Count,
-							bytes.Count(s, []byte("c")),
+							CMutant:        seq.Count,
-							bytes.Count(s, []byte("g")),
+							Pos:            edge.Pos,
-							bytes.Count(s, []byte("t"))})
+							Length:         father.Sequence.Len(),
+							A:              bytes.Count(s, []byte("a")),
+							C:              bytes.Count(s, []byte("c")),
+							G:              bytes.Count(s, []byte("g")),
+							T:              bytes.Count(s, []byte("t"))})
 				}
 			}
 

pkg/obiutils/set.go

@@ -23,7 +23,7 @@ func MakeSet[E comparable](vals ...E) Set[E] {
 // It takes a variadic parameter of type E, where E is a comparable type.
 // It returns a pointer to a Set of type E.
 func NewSet[E comparable](vals ...E) *Set[E] {
-	s := MakeSet[E](vals...)
+	s := MakeSet(vals...)
 	return &s
 }
 

pkg/obiutils/set_test.go

@@ -50,7 +50,7 @@ func TestNewSet(t *testing.T) {
 	}
 
 	// Test Case 2: Creating a set with multiple values
-	set2 := NewSet[string]("apple", "banana", "cherry")
+	set2 := NewSet("apple", "banana", "cherry")
 	if len(*set2) != 3 {
 		t.Errorf("Expected size to be 3, but got %d", len(*set2))
 	}
@@ -147,7 +147,7 @@ func TestMembers(t *testing.T) {
 	}
 
 	// Test case 2: Set with multiple elements
-	set = MakeSet[int](1, 2, 3)
+	set = MakeSet(1, 2, 3)
 	expected = []int{1, 2, 3}
 	actual = set.Members()
 	sort.Ints(actual)
@@ -172,7 +172,7 @@ func TestSetString(t *testing.T) {
 	}
 
 	// Test set with single member
-	singleMemberSet := NewSet[int](42)
+	singleMemberSet := NewSet(42)
 	singleMemberSetString := singleMemberSet.String()
 	expectedSingleMemberSetString := "[42]"
 	if singleMemberSetString != expectedSingleMemberSetString {
@@ -180,7 +180,7 @@ func TestSetString(t *testing.T) {
 	}
 
 	// Test set with multiple members
-	multipleMembersSet := NewSet[int](1, 2, 3)
+	multipleMembersSet := NewSet(1, 2, 3)
 	multipleMembersSetString := multipleMembersSet.String()
 	expectedMultipleMembersSetString := "[1 2 3]"
 	if multipleMembersSetString != expectedMultipleMembersSetString {
@@ -213,26 +213,26 @@ func TestUnion(t *testing.T) {
 
 	// Test case 2: Union of an empty set and a non-empty set should return the non-empty set
 	set1 = MakeSet[int]()
-	set2 = MakeSet[int](1, 2, 3)
+	set2 = MakeSet(1, 2, 3)
-	expected = MakeSet[int](1, 2, 3)
+	expected = MakeSet(1, 2, 3)
 	result = set1.Union(set2)
 	if !reflect.DeepEqual(result, expected) {
 		t.Errorf("Expected %v, but got %v", expected, result)
 	}
 
 	// Test case 3: Union of two non-empty sets with common elements should return a set with unique elements
-	set1 = MakeSet[int](1, 2, 3)
+	set1 = MakeSet(1, 2, 3)
-	set2 = MakeSet[int](2, 3, 4)
+	set2 = MakeSet(2, 3, 4)
-	expected = MakeSet[int](1, 2, 3, 4)
+	expected = MakeSet(1, 2, 3, 4)
 	result = set1.Union(set2)
 	if !reflect.DeepEqual(result, expected) {
 		t.Errorf("Expected %v, but got %v", expected, result)
 	}
 
 	// Test case 4: Union of two non-empty sets with no common elements should return a set with all elements
-	set1 = MakeSet[int](1, 2, 3)
+	set1 = MakeSet(1, 2, 3)
-	set2 = MakeSet[int](4, 5, 6)
+	set2 = MakeSet(4, 5, 6)
-	expected = MakeSet[int](1, 2, 3, 4, 5, 6)
+	expected = MakeSet(1, 2, 3, 4, 5, 6)
 	result = set1.Union(set2)
 	if !reflect.DeepEqual(result, expected) {
 		t.Errorf("Expected %v, but got %v", expected, result)