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Patch some bugs in writing files

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Former-commit-id: 612868a281dc0ecf4e6c5776973735e5c71bd517
This commit is contained in:
Eric Coissac
2024-06-19 13:15:30 +02:00
parent 73996bb0b7
commit 818ce87bab
8 changed files with 75 additions and 22 deletions
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38
pkg/obiformats/fastseq_write_fastq.go
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@@ -32,17 +32,31 @@ func FormatFastq(seq *obiseq.BioSequence, formater FormatHeader) string {
q,
)
if f[0] != '@' {
log.Panicln("FormatFastq: FASTQ format error")
}
return f
}
func FormatFastqBatch(batch obiiter.BioSequenceBatch,
formater FormatHeader, skipEmpty bool) []byte {
var bs bytes.Buffer
for _, seq := range batch.Slice() {
if seq.Len() > 0 {
fs := FormatFastq(seq, formater)
bs.WriteString(fs)
lb := bs.Len()
n, _ := bs.WriteString(fs)
if n < len(fs) {
log.Panicln("FormatFastqBatch: Cannot write all FASTQ sequences")
}
bs.WriteString("\n")
if bs.Len()-lb < len(fs)+1 {
log.Panicln("FormatFastqBatch: Cannot write all FASTQ sequences correctly")
}
} else {
if skipEmpty {
log.Warnf("Sequence %s is empty and skiped in output", seq.Id())
@@ -53,7 +67,15 @@ func FormatFastqBatch(batch obiiter.BioSequenceBatch,
}
return bs.Bytes()
chunk := bs.Bytes()
chunk = chunk[:bs.Len()]
if chunk[0] != '@' {
log.Panicln("FormatFastqBatch: FASTQ format error")
}
return chunk
}
type FileChunck struct {
@@ -118,16 +140,25 @@ func WriteFastq(iterator obiiter.IBioSequence,
go func() {
for chunk := range chunkchan {
if chunk.order == next_to_send {
if chunk.text[0] != '@' {
log.Panicln("WriteFastq: FASTQ format error")
}
file.Write(chunk.text)
next_to_send++
chunk, ok := received[next_to_send]
for ok {
if chunk.text[0] != '@' {
log.Panicln("WriteFastq: FASTQ format error")
}
file.Write(chunk.text)
delete(received, next_to_send)
next_to_send++
chunk, ok = received[next_to_send]
}
} else {
if _, ok := received[chunk.order]; ok {
log.Panicln("WriteFastq: Two chunks with the same number")
}
received[chunk.order] = chunk
}
@@ -158,7 +189,10 @@ func WriteFastqToFile(iterator obiiter.IBioSequence,
if opt.AppendFile() {
flags |= os.O_APPEND
} else {
flags |= os.O_TRUNC
}
file, err := os.OpenFile(filename, flags, 0660)
if err != nil {