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

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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
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12
pkg/obiformats/ecopcr_read.go
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@ -7,6 +7,7 @@ import (
"fmt"
"io"
"os"
"path"
"strconv"
"strings"
@ -14,6 +15,7 @@ import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
)
type __ecopcr_file__ struct {
@ -177,6 +179,7 @@ func ReadEcoPCR(reader io.Reader, options ...WithOption) obiiter.IBioSequence {
go func() {
seq, err := __read_ecopcr_bioseq__(&ecopcr)
seq.SetSource(opt.Source())
slice := make(obiseq.BioSequenceSlice, 0, opt.BatchSize())
i := 0
ii := 0
@ -191,6 +194,7 @@ func ReadEcoPCR(reader io.Reader, options ...WithOption) obiiter.IBioSequence {
}
seq, err = __read_ecopcr_bioseq__(&ecopcr)
seq.SetSource(opt.Source())
}
if len(slice) > 0 {
@ -205,14 +209,20 @@ func ReadEcoPCR(reader io.Reader, options ...WithOption) obiiter.IBioSequence {
}()
if opt.pointer.full_file_batch {
newIter = newIter.FullFileIterator()
}
return newIter
}
func ReadEcoPCRBatchFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
func ReadEcoPCRFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
var reader io.Reader
var greader io.Reader
var err error
options = append(options, OptionsSource(obiutils.RemoveAllExt((path.Base(filename)))))
reader, err = os.Open(filename)
if err != nil {
log.Printf("open file error: %+v", err)