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Patch reading of annotation from stdin

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This commit is contained in:
Eric Coissac
2022-09-29 14:48:05 +02:00
parent d0f63fda56
commit 65210755cc
3 changed files with 17 additions and 5 deletions
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12
pkg/obiformats/fastseq_read.go
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@@ -26,8 +26,7 @@ func _FastseqReader(seqfile C.fast_kseq_p,
slice := obiseq.MakeBioSequenceSlice()
for l := int64(C.next_fast_sek(seqfile)); l > 0; l = int64(C.next_fast_sek(seqfile)) {
for l := int64(C.next_fast_sek(seqfile)); l != 0; l = int64(C.next_fast_sek(seqfile)) {
s := seqfile.seq
sequence := C.GoBytes(unsafe.Pointer(s.seq.s), C.int(s.seq.l))
@@ -77,6 +76,9 @@ func _FastseqReader(seqfile C.fast_kseq_p,
i++
ii = 0
}
// log.Println("longueur : ",l,rep.Length())
}
if len(slice) > 0 {
iterator.Push(obiiter.MakeBioSequenceBatch(i, slice))
@@ -148,6 +150,12 @@ func ReadFastSeqBatchFromStdin(options ...WithOption) obiiter.IBioSequenceBatch
go _FastseqReader(C.open_fast_sek_stdin(C.int32_t(opt.QualityShift())),
newIter, opt.BatchSize())
parser := opt.ParseFastSeqHeader()
if parser != nil {
return IParseFastSeqHeaderBatch(newIter, options...)
}
return newIter
}