Patch a tricky bug in parsing of json header and save the last sequence from files

Former-commit-id: bfe3d0e9eb8e65113699d535bd1d9a5fe0d3ce1d

pkg/obiformats/fastseq_json_header.go

@@ -12,7 +12,6 @@ import (
 )
 
 func _parse_json_header_(header string, annotations obiseq.Annotation) string {
-
 	start := -1
 	stop := -1
 	level := 0
@@ -58,6 +57,9 @@ func _parse_json_header_(header string, annotations obiseq.Annotation) string {
 			if vt == math.Floor(vt) {
 				annotations[k] = int(vt)
 			}
+			{
+				annotations[k] = vt
+			}
 		}
 	}
 
@@ -69,8 +71,18 @@ func _parse_json_header_(header string, annotations obiseq.Annotation) string {
 }
 
 func ParseFastSeqJsonHeader(sequence *obiseq.BioSequence) {
-	sequence.SetDefinition(_parse_json_header_(sequence.Definition(),
-		sequence.Annotations()))
+	definition := sequence.Definition()
+	sequence.SetDefinition("")
+
+	definition_part := _parse_json_header_(
+		definition,
+		sequence.Annotations())
+	if len(definition_part) > 0 {
+		if sequence.HasDefinition() {
+			definition_part = sequence.Definition() + " " + definition_part
+		}
+		sequence.SetDefinition(definition_part)
+	}
 }
 
 func FormatFastSeqJsonHeader(sequence *obiseq.BioSequence) string {
@@ -80,7 +92,7 @@ func FormatFastSeqJsonHeader(sequence *obiseq.BioSequence) string {
 		text, err := obiutils.JsonMarshal(sequence.Annotations())
 
 		if err != nil {
-			panic(err)
+			log.Fatal(err)
 		}
 
 		return string(text)

pkg/obiformats/fastseq_obi_header.go

@@ -285,11 +285,17 @@ func ParseOBIFeatures(text string, annotations obiseq.Annotation) string {
 
 func ParseFastSeqOBIHeader(sequence *obiseq.BioSequence) {
 	annotations := sequence.Annotations()
+	definition := sequence.Definition()
+	sequence.SetDefinition("")
 
-	definition := ParseOBIFeatures(sequence.Definition(),
-		annotations)
+	definition = ParseOBIFeatures(definition, annotations)
 
-	sequence.SetDefinition(definition)
+	if len(definition) > 0 {
+		if sequence.HasDefinition() {
+			definition = sequence.Definition() + " " + definition
+		}
+		sequence.SetDefinition(definition)
+	}
 }
 
 func FormatFastSeqOBIHeader(sequence *obiseq.BioSequence) string {

pkg/obiformats/seqfile_chunck_read.go

@@ -106,6 +106,16 @@ func ReadSeqFileChunk(reader io.Reader,
 			}
 		}
 
+		if err != nil && err != io.EOF && err != io.ErrUnexpectedEOF {
+			log.Fatalf("Error reading data from file : %s", err)
+		}
+
+		// Send the last chunk to the channel
+		if len(buff) > 0 {
+			io := bytes.NewBuffer(slices.Clone(buff))
+			chunk_channel <- SeqFileChunk{io, i}
+		}
+
 		// Close the readers channel when the end of the file is reached
 		close(chunk_channel)
 	}()

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 = "f4fcc19"
+var _Commit = "b842d60"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.