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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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19
pkg/obiformats/fastaseq_read.go
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@@ -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))
}
}