obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

First attempt for obiconsensus... The graph traversing algorithm is too simple

Browse Source 
Former-commit-id: 0456e6c7fd55d6d0fcf9856c40386b976b912cba
This commit is contained in:
Eric Coissac
2023-03-27 19:51:10 +07:00
parent d5e84ec676
commit a33e471b39
17 changed files with 868 additions and 23 deletions
Download Patch File Download Diff File Expand all files Collapse all files

45
pkg/obiformats/fastseq_read.go
View File

@ -10,15 +10,18 @@ import (
"bytes"
"fmt"
"os"
"path"
"unsafe"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
)
func _FastseqReader(seqfile C.fast_kseq_p,
func _FastseqReader(source string,
seqfile C.fast_kseq_p,
iterator obiiter.IBioSequence,
batch_size int) {
var comment string
@ -40,7 +43,7 @@ func _FastseqReader(seqfile C.fast_kseq_p,
}
rep := obiseq.NewBioSequence(name, bytes.ToLower(sequence), comment)
rep.SetSource(source)
if s.qual.l > C.ulong(0) {
cquality := unsafe.Slice(s.qual.s, C.int(s.qual.l))
l := int(s.qual.l)
@ -81,6 +84,9 @@ func _FastseqReader(seqfile C.fast_kseq_p,
}
func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
options = append(options, OptionsSource(obiutils.RemoveAllExt((path.Base(filename)))))
opt := MakeOptions(options)
name := C.CString(filename)
@ -108,14 +114,20 @@ func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSe
newIter := obiiter.MakeIBioSequence()
newIter.Add(1)
go func() {
newIter.WaitAndClose()
log.Debugln("End of the fastq file reading")
}()
go func(iter obiiter.IBioSequence) {
iter.WaitAndClose()
log.Debugln("End of the fastx file reading")
}(newIter)
log.Debugln("Start of the fastq file reading")
log.Debugln("Start of the fastx file reading")
go _FastseqReader(opt.Source(), pointer, newIter, opt.BatchSize())
log.Debugln("Full file batch mode : ", opt.FullFileBatch())
if opt.FullFileBatch() {
newIter = newIter.FullFileIterator()
}
go _FastseqReader(pointer, newIter, opt.BatchSize())
parser := opt.ParseFastSeqHeader()
if parser != nil {
@ -126,18 +138,27 @@ func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSe
}
func ReadFastSeqFromStdin(options ...WithOption) obiiter.IBioSequence {
options = append(options, OptionsSource("stdin"))
opt := MakeOptions(options)
newIter := obiiter.MakeIBioSequence()
newIter.Add(1)
go func() {
newIter.WaitAndClose()
}()
go func(iter obiiter.IBioSequence) {
iter.WaitAndClose()
}(newIter)
go _FastseqReader(C.open_fast_sek_stdin(C.int32_t(opt.QualityShift())),
go _FastseqReader(opt.Source(),
C.open_fast_sek_stdin(C.int32_t(opt.QualityShift())),
newIter, opt.BatchSize())
log.Debugln("Full file batch mode : ", opt.FullFileBatch())
if opt.FullFileBatch() {
newIter = newIter.FullFileIterator()
}
parser := opt.ParseFastSeqHeader()
if parser != nil {