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

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Former-commit-id: b842d60af9c2f1f971946d99999d13cfc15793b3
This commit is contained in:
Eric Coissac
2024-06-04 11:57:16 +02:00
parent 411124d1b3
commit aa42df326a
6 changed files with 104 additions and 42 deletions
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16
pkg/obiseq/biosequence.go
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@@ -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.