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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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17
pkg/obiformats/ecopcr_read.go
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@ -10,6 +10,7 @@ import (
"strconv"
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
@ -117,7 +118,7 @@ func __read_ecopcr_bioseq__(file *__ecopcr_file__) (*obiseq.BioSequence, error)
return bseq, nil
}
func ReadEcoPCRBatch(reader io.Reader, options ...WithOption) obiseq.IBioSequenceBatch {
func ReadEcoPCRBatch(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch {
tag := make([]byte, 11)
n, _ := reader.Read(tag)
@ -163,7 +164,7 @@ func ReadEcoPCRBatch(reader io.Reader, options ...WithOption) obiseq.IBioSequenc
opt := MakeOptions(options)
newIter := obiseq.MakeIBioSequenceBatch(opt.BufferSize())
newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize())
newIter.Add(1)
go func() {
@ -181,7 +182,7 @@ func ReadEcoPCRBatch(reader io.Reader, options ...WithOption) obiseq.IBioSequenc
slice = append(slice, seq)
ii++
if ii >= opt.BatchSize() {
newIter.Push(obiseq.MakeBioSequenceBatch(i, slice))
newIter.Push(obiiter.MakeBioSequenceBatch(i, slice))
slice = obiseq.MakeBioSequenceSlice()
i++
ii = 0
@ -191,7 +192,7 @@ func ReadEcoPCRBatch(reader io.Reader, options ...WithOption) obiseq.IBioSequenc
}
if len(slice) > 0 {
newIter.Push(obiseq.MakeBioSequenceBatch(i, slice))
newIter.Push(obiiter.MakeBioSequenceBatch(i, slice))
}
newIter.Done()
@ -205,12 +206,12 @@ func ReadEcoPCRBatch(reader io.Reader, options ...WithOption) obiseq.IBioSequenc
return newIter
}
func ReadEcoPCR(reader io.Reader, options ...WithOption) obiseq.IBioSequence {
func ReadEcoPCR(reader io.Reader, options ...WithOption) obiiter.IBioSequence {
ib := ReadEcoPCRBatch(reader, options...)
return ib.SortBatches().IBioSequence()
}
func ReadEcoPCRBatchFromFile(filename string, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
func ReadEcoPCRBatchFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) {
var reader io.Reader
var greader io.Reader
var err error
@ -218,7 +219,7 @@ func ReadEcoPCRBatchFromFile(filename string, options ...WithOption) (obiseq.IBi
reader, err = os.Open(filename)
if err != nil {
log.Printf("open file error: %+v", err)
return obiseq.NilIBioSequenceBatch, err
return obiiter.NilIBioSequenceBatch, err
}
// Test if the flux is compressed by gzip
@ -230,7 +231,7 @@ func ReadEcoPCRBatchFromFile(filename string, options ...WithOption) (obiseq.IBi
return ReadEcoPCRBatch(reader, options...), nil
}
func ReadEcoPCRFromFile(filename string, options ...WithOption) (obiseq.IBioSequence, error) {
func ReadEcoPCRFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
ib, err := ReadEcoPCRBatchFromFile(filename, options...)
return ib.SortBatches().IBioSequence(), err