Correct a bug in the fastq reader affecting the quality of the last record of each chunk

Former-commit-id: b842d60af9c2f1f971946d99999d13cfc15793b3

pkg/obiformats/fastaseq_read.go

@@ -6,7 +6,6 @@ import (
 	"io"
 	"os"
 	"path"
-	"slices"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
@@ -155,7 +154,11 @@ func _ParseFastaFile(source string,
 				if C == '>' {
 					if previous == '\r' || previous == '\n' {
 						// End of sequence
-						s := obiseq.NewBioSequence(identifier, slices.Clone(seqBytes.Bytes()), definition)
+						rawseq := seqBytes.Bytes()
+						if len(rawseq) == 0 {
+							log.Fatalf("@%s[%s] : sequence is empty", identifier, source)
+						}
+						s := obiseq.NewBioSequence(identifier, rawseq, definition)
 						s.SetSource(source)
 						sequences = append(sequences, s)
 						if no_order {
@@ -198,17 +201,21 @@ func _ParseFastaFile(source string,
 		}
 
 		if state == 6 {
-			s := obiseq.NewBioSequence(identifier, slices.Clone(seqBytes.Bytes()), definition)
+			rawseq := seqBytes.Bytes()
+			if len(rawseq) == 0 {
+				log.Fatalf("@%s[%s] : sequence is empty", identifier, source)
+			}
+			s := obiseq.NewBioSequence(identifier, rawseq, definition)
 			s.SetSource(source)
 			sequences = append(sequences, s)
 		}
 
 		if len(sequences) > 0 {
+			co := chunks.order
 			if no_order {
-				out.Push(obiiter.MakeBioSequenceBatch(chunck_order(), sequences))
-			} else {
-				out.Push(obiiter.MakeBioSequenceBatch(chunks.order, sequences))
+				co = chunck_order()
 			}
+			out.Push(obiiter.MakeBioSequenceBatch(co, sequences))
 		}
 	}
 

pkg/obiformats/fastqseq_read.go

@@ -6,7 +6,6 @@ import (
 	"io"
 	"os"
 	"path"
-	"slices"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
@@ -97,9 +96,27 @@ func _EndOfLastFastqEntry(buffer []byte) int {
 	if i == 0 || state != 7 {
 		return -1
 	}
+
 	return cut
 }
 
+func _storeSequenceQuality(bytes *bytes.Buffer, out *obiseq.BioSequence, quality_shift byte) {
+	q := bytes.Bytes()
+	if len(q) == 0 {
+		log.Fatalf("@%s[%s] : sequence quality is empty", out.Id(), out.Source())
+	}
+
+	if len(q) != out.Len() {
+		log.Fatalf("%s[%s] : sequence data and quality lenght not equal (%d <> %d)",
+			out.Id(), out.Source(), len(q), out.Len())
+	}
+
+	for i := 0; i < len(q); i++ {
+		q[i] = q[i] - quality_shift
+	}
+	out.SetQualities(q)
+}
+
 func _ParseFastqFile(source string,
 	input ChannelSeqFileChunk,
 	out obiiter.IBioSequence,
@@ -122,6 +139,8 @@ func _ParseFastqFile(source string,
 	for chunks := range input {
 		scanner := bufio.NewReader(chunks.raw)
 		sequences := make(obiseq.BioSequenceSlice, 0, 100)
+		previous := byte(0)
+
 		for C, err := scanner.ReadByte(); err != io.EOF; C, err = scanner.ReadByte() {
 
 			is_end_of_line := C == '\r' || C == '\n'
@@ -135,12 +154,12 @@ func _ParseFastqFile(source string,
 					// Beginning of sequence
 					state = 1
 				} else {
-					log.Errorf("%s : sequence entry is not starting with @", source)
+					log.Fatalf("%s : sequence entry is not starting with @", source)
 				}
 			case 1: // Beginning of identifier (Mandatory)
 				if is_sep {
 					// No identifier -> ERROR
-					log.Errorf("%s : sequence identifier is empty", source)
+					log.Fatalf("%s : sequence identifier is empty", source)
 				} else {
 					// Beginning of identifier
 					state = 2
@@ -191,7 +210,11 @@ func _ParseFastqFile(source string,
 			case 6:
 				if is_end_of_line {
 					// End of sequence
-					s := obiseq.NewBioSequence(identifier, slices.Clone(seqBytes.Bytes()), definition)
+					rawseq := seqBytes.Bytes()
+					if len(rawseq) == 0 {
+						log.Fatalf("@%s[%s] : sequence is empty", identifier, source)
+					}
+					s := obiseq.NewBioSequence(identifier, rawseq, definition)
 					s.SetSource(source)
 					sequences = append(sequences, s)
 					state = 7
@@ -199,7 +222,16 @@ func _ParseFastqFile(source string,
 					if C >= 'A' && C <= 'Z' {
 						C = C + 'a' - 'A'
 					}
-					seqBytes.WriteByte(C)
+					if (C >= 'a' && C <= 'z') || C == '-' || C == '.' || C == '[' || C == ']' {
+						seqBytes.WriteByte(C)
+					} else {
+						context, _ := scanner.Peek(30)
+						context = append(
+							append([]byte{previous}, C),
+							context...)
+						log.Fatalf("%s [%s]: sequence contains invalid character %c (%s)",
+							source, identifier, C, string(context))
+					}
 				}
 			case 7:
 				if is_end_of_line {
@@ -207,9 +239,10 @@ func _ParseFastqFile(source string,
 				} else if C == '+' {
 					state = 8
 				} else {
-					log.Errorf("@%s[%s] : sequence data not followed by a line starting with + but a %c", identifier, source, C)
+					log.Fatalf("@%s[%s] : sequence data not followed by a line starting with + but a %c", identifier, source, C)
 				}
 			case 8:
+				// State consuming the + internal header line
 				if is_end_of_line {
 					state = 9
 				}
@@ -224,16 +257,7 @@ func _ParseFastqFile(source string,
 				}
 			case 10:
 				if is_end_of_line {
-					// End of quality
-					q := qualBytes.Bytes()
-					if len(q) != sequences[len(sequences)-1].Len() {
-						log.Errorf("%s[%s] : sequence data and quality lenght not equal (%d/%d)",
-							identifier, source, len(q), sequences[len(sequences)-1].Len())
-					}
-					for i := 0; i < len(q); i++ {
-						q[i] = q[i] - quality_shift
-					}
-					sequences[len(sequences)-1].SetQualities(q)
+					_storeSequenceQuality(qualBytes, sequences[len(sequences)-1], quality_shift)
 
 					if no_order {
 						if len(sequences) == batch_size {
@@ -252,18 +276,25 @@ func _ParseFastqFile(source string,
 				} else if C == '@' {
 					state = 1
 				} else {
-					log.Errorf("%s[%s] : sequence record not followed by a line starting with @", identifier, source)
+					log.Fatalf("%s[%s] : sequence record not followed by a line starting with @", identifier, source)
 				}
 
 			}
+
+			previous = C
 		}
 
 		if len(sequences) > 0 {
-			if no_order {
-				out.Push(obiiter.MakeBioSequenceBatch(chunck_order(), sequences))
-			} else {
-				out.Push(obiiter.MakeBioSequenceBatch(chunks.order, sequences))
+			if state == 10 {
+				_storeSequenceQuality(qualBytes, sequences[len(sequences)-1], quality_shift)
+				state = 1
 			}
+
+			co := chunks.order
+			if no_order {
+				co = chunck_order()
+			}
+			out.Push(obiiter.MakeBioSequenceBatch(co, sequences))
 		}
 
 	}

pkg/obiformats/seqfile_chunck_read.go

@@ -91,11 +91,6 @@ func ReadSeqFileChunk(reader io.Reader,
 					io := bytes.NewBuffer(slices.Clone(buff))
 					chunk_channel <- SeqFileChunk{io, i}
 					i++
-
-					// if string(buff[io.Len()-2:]) != "//" {
-					// 	log.Fatalf("File chunck ends with 3 bytes : %s", io.Bytes()[io.Len()-3:])
-					// }
-
 				}
 
 				if lremain > 0 {

pkg/obioptions/version.go

@@ -4,7 +4,10 @@ import (
 	"fmt"
 )
 
-var _Commit = ""
+// 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 _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.

pkg/obiseq/biosequence.go

@@ -273,19 +273,19 @@ func (s *BioSequence) Qualities() Quality {
 // Returns a string representing the qualities of the BioSequence after applying the shift.
 func (s *BioSequence) QualitiesString() string {
 	quality_shift := obioptions.OutputQualityShift()
+
 	qual := s.Qualities()
-	qual_ascii := make([]byte, len(qual))
+	qual_ascii := GetSlice(len(qual))[0:len(qual)]
 	for i := 0; i < len(qual); i++ {
 		quality := qual[i]
-		if quality < 0 {
-			quality = 0
-		}
 		if quality > 93 {
 			quality = 93
 		}
 		qual_ascii[i] = quality + quality_shift
 	}
-	return string(qual_ascii)
+	qual_sting := string(qual_ascii)
+	RecycleSlice(&qual_ascii)
+	return qual_sting
 }
 
 // Features returns the feature string of the BioSequence.
@@ -420,7 +420,8 @@ func (s *BioSequence) SetSequence(sequence []byte) {
 	if s.sequence != nil {
 		RecycleSlice(&s.sequence)
 	}
-	s.sequence = obiutils.InPlaceToLower(sequence)
+	s.sequence = GetSlice(len(sequence))[0:len(sequence)]
+	copy(s.sequence, obiutils.InPlaceToLower(sequence))
 }
 
 // Setting the qualities of the BioSequence.
@@ -428,7 +429,8 @@ func (s *BioSequence) SetQualities(qualities Quality) {
 	if s.qualities != nil {
 		RecycleSlice(&s.qualities)
 	}
-	s.qualities = qualities
+	s.qualities = GetSlice(len(qualities))[0:len(qualities)]
+	copy(s.qualities, qualities)
 }
 
 // A method that appends a byte slice to the qualities of the BioSequence.

pkg/obiseq/pool.go

@@ -15,6 +15,17 @@ var _BioSequenceByteSlicePool = sync.Pool{
 	},
 }
 
+// RecycleSlice recycles a byte slice by clearing its contents and returning it
+// to a pool if it is small enough.
+//
+// Parameters: - s: a pointer to a byte slice that will be recycled.
+//
+// This function first checks if the input slice is not nil and has a non-zero
+// capacity. If so, it clears the contents of the slice by setting its length to
+// 0. Then, it checks if the capacity of the slice is less than or equal to
+// 1024. If it is, the function puts the slice into a pool for reuse. If the
+// capacity is 0 or greater than 1024, the function does nothing. If the input
+// slice is nil or has a zero capacity, the function logs a panic message.
 func RecycleSlice(s *[]byte) {
 	if s != nil && cap(*s) > 0 {
 		*s = (*s)[:0]
@@ -27,9 +38,22 @@ func RecycleSlice(s *[]byte) {
 	}
 }
 
-// It returns a slice of bytes from a pool of slices.
+// GetSlice returns a byte slice with the specified capacity.
 //
-// the slice can be prefilled with the provided values
+// The function first checks if the capacity is less than or equal to 1024. If it is,
+// it retrieves a byte slice from the _BioSequenceByteSlicePool. If the retrieved
+// slice is nil, has a nil underlying array, or has a capacity less than the
+// specified capacity, a new byte slice is created with the specified capacity.
+// If the capacity is greater than 1024, a new byte slice is created with the
+// specified capacity.
+//
+// The function returns the byte slice.
+//
+// Parameters:
+// - capacity: the desired capacity of the byte slice.
+//
+// Return type:
+// - []byte: the byte slice with the specified capacity.
 func GetSlice(capacity int) []byte {
 	p := (*[]byte)(nil)
 	if capacity <= 1024 {