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A global version of a Slice pool

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This commit is contained in:
Eric Coissac
2022-01-16 00:21:42 +01:00
parent e1b7e1761c
commit 576a9f4d2d
11 changed files with 227 additions and 149 deletions
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2
pkg/obiformats/embl_read.go
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@@ -128,7 +128,7 @@ func _ParseEmblFile(input <-chan _FileChunk, out obiseq.IBioSequenceBatch) {
seqBytes.Bytes(),
defBytes.String())
sequence.SetFeatures(featBytes.String())
sequence.SetFeatures(featBytes.Bytes())
annot := sequence.Annotations()
annot["scientific_name"] = scientificName

18
pkg/obiformats/fastseq_read.go
View File

@@ -17,7 +17,7 @@ import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
func __fastseq_reader__(seqfile C.fast_kseq_p,
func _FastseqReader(seqfile C.fast_kseq_p,
iterator obiseq.IBioSequenceBatch,
batch_size int) {
var comment string
@@ -30,8 +30,12 @@ func __fastseq_reader__(seqfile C.fast_kseq_p,
s := seqfile.seq
sequence := C.GoBytes(unsafe.Pointer(s.seq.s),
C.int(s.seq.l))
csequence := cutils.ByteSlice(unsafe.Pointer(s.seq.s), int(s.seq.l))
sequence := obiseq.GetSlice()
sequence = append(sequence, csequence...)
//sequence := C.GoBytes(unsafe.Pointer(s.seq.s),
// C.int(s.seq.l))
name := C.GoString(s.name.s)
@@ -45,11 +49,11 @@ func __fastseq_reader__(seqfile C.fast_kseq_p,
if s.qual.l > C.ulong(0) {
cquality := cutils.ByteSlice(unsafe.Pointer(s.qual.s), int(s.qual.l))
quality := make(obiseq.Quality, s.qual.l)
l := int(s.qual.l)
quality := obiseq.GetSlice()
shift := uint8(seqfile.shift)
for j := 0; j < l; j++ {
quality[j] = uint8(cquality[j]) - shift
quality = append(quality, uint8(cquality[j])-shift)
}
rep.SetQualities(quality)
@@ -116,7 +120,7 @@ func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiseq.IB
log.Println("Start of the fastq file reading")
go __fastseq_reader__(pointer, newIter, opt.BatchSize())
go _FastseqReader(pointer, newIter, opt.BatchSize())
parser := opt.ParseFastSeqHeader()
if parser != nil {
return IParseFastSeqHeaderBatch(newIter, options...), err
@@ -141,7 +145,7 @@ func ReadFastSeqBatchFromStdin(options ...WithOption) obiseq.IBioSequenceBatch {
close(newIter.Channel())
}()
go __fastseq_reader__(C.open_fast_sek_stdin(C.int32_t(opt.QualityShift())), newIter, opt.BatchSize())
go _FastseqReader(C.open_fast_sek_stdin(C.int32_t(opt.QualityShift())), newIter, opt.BatchSize())
return newIter
}