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Produce less weird crash on non existing files

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Former-commit-id: 74bb27bd53c685be530632994bd2ba24c1f362e1
This commit is contained in:
Eric Coissac
2023-03-07 17:34:25 +07:00
parent fbfed52508
commit b3922c3896
21 changed files with 147 additions and 32 deletions
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11
pkg/obiformats/genbank_read.go
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@ -47,7 +47,7 @@ func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequence) {
nl++
line := scanner.Text()
switch {
case state==inDefinition && ! strings.HasPrefix(line, " "):
case state == inDefinition && !strings.HasPrefix(line, " "):
state = inEntry
fallthrough
case strings.HasPrefix(line, "LOCUS "):
@ -61,7 +61,7 @@ func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequence) {
case strings.HasPrefix(line, "FEATURES "):
featBytes.WriteString(line)
state = inFeature
case strings.HasPrefix(line, "ORIGIN "):
case strings.HasPrefix(line, "ORIGIN"):
state = inSequence
case line == "//":
log.Debugln("Total lines := ", nl)
@ -76,12 +76,15 @@ func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequence) {
annot["scientific_name"] = scientificName
annot["taxid"] = taxid
// log.Println(FormatFasta(sequence, FormatFastSeqJsonHeader))
log.Debugf("Read sequences %s: %dbp (%d)", sequence.Id(),
sequence.Len(), seqBytes.Len())
sequences = append(sequences, sequence)
defBytes = new(bytes.Buffer)
featBytes = new(bytes.Buffer)
seqBytes = new(bytes.Buffer)
nl=0
sl=0
nl = 0
sl = 0
default:
switch state {
case inDefinition: