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Some code refactoring, a new version of obiuniq more efficient in memory and a first make file allowing to build obitools

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This commit is contained in:
Eric Coissac
2022-02-24 07:08:40 +01:00
parent 2e7c1834b0
commit eaf65fbcce
39 changed files with 1225 additions and 241 deletions
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24
pkg/obiformats/fastseq_read.go
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@ -13,11 +13,12 @@ import (
"unsafe"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/cutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
func _FastseqReader(seqfile C.fast_kseq_p,
iterator obiseq.IBioSequenceBatch,
iterator obiiter.IBioSequenceBatch,
batch_size int) {
var comment string
i := 0
@ -63,7 +64,7 @@ func _FastseqReader(seqfile C.fast_kseq_p,
// log.Printf("\n==> Pushing sequence batch\n")
// start := time.Now()
iterator.Push(obiseq.MakeBioSequenceBatch(i, slice))
iterator.Push(obiiter.MakeBioSequenceBatch(i, slice))
// elapsed := time.Since(start)
// log.Printf("\n==>sequences pushed after %s\n", elapsed)
@ -73,13 +74,13 @@ func _FastseqReader(seqfile C.fast_kseq_p,
}
}
if len(slice) > 0 {
iterator.Push(obiseq.MakeBioSequenceBatch(i, slice))
iterator.Push(obiiter.MakeBioSequenceBatch(i, slice))
}
iterator.Done()
}
func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) {
opt := MakeOptions(options)
name := C.CString(filename)
@ -92,7 +93,7 @@ func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiseq.IB
if pointer == nil {
err = fmt.Errorf("cannot open file %s", filename)
return obiseq.NilIBioSequenceBatch, err
return obiiter.NilIBioSequenceBatch, err
}
size := int64(-1)
@ -104,7 +105,7 @@ func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiseq.IB
size = -1
}
newIter := obiseq.MakeIBioSequenceBatch(opt.BufferSize())
newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize())
newIter.Add(1)
go func() {
@ -124,14 +125,14 @@ func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiseq.IB
return newIter, err
}
func ReadFastSeqFromFile(filename string, options ...WithOption) (obiseq.IBioSequence, error) {
func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
ib, err := ReadFastSeqBatchFromFile(filename, options...)
return ib.SortBatches().IBioSequence(), err
}
func ReadFastSeqBatchFromStdin(options ...WithOption) obiseq.IBioSequenceBatch {
func ReadFastSeqBatchFromStdin(options ...WithOption) obiiter.IBioSequenceBatch {
opt := MakeOptions(options)
newIter := obiseq.MakeIBioSequenceBatch(opt.BufferSize())
newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize())
newIter.Add(1)
@ -139,12 +140,13 @@ func ReadFastSeqBatchFromStdin(options ...WithOption) obiseq.IBioSequenceBatch {
newIter.WaitAndClose()
}()
go _FastseqReader(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
}
func ReadFastSeqFromStdin(options ...WithOption) obiseq.IBioSequence {
func ReadFastSeqFromStdin(options ...WithOption) obiiter.IBioSequence {
ib := ReadFastSeqBatchFromStdin(options...)
return ib.SortBatches().IBioSequence()
}