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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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14
pkg/obiformats/universal_read.go
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@ -8,7 +8,7 @@ import (
"os"
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
)
func GuessSeqFileType(firstline string) string {
@ -36,7 +36,8 @@ func GuessSeqFileType(firstline string) string {
}
}
func ReadSequencesBatchFromFile(filename string, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
func ReadSequencesBatchFromFile(filename string,
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
var file *os.File
var reader io.Reader
var greader io.Reader
@ -46,7 +47,7 @@ func ReadSequencesBatchFromFile(filename string, options ...WithOption) (obiseq.
if err != nil {
log.Fatalf("open file error: %v", err)
return obiseq.NilIBioSequenceBatch, err
return obiiter.NilIBioSequenceBatch, err
}
reader = file
@ -65,7 +66,7 @@ func ReadSequencesBatchFromFile(filename string, options ...WithOption) (obiseq.
tag, _ := breader.Peek(30)
if len(tag) < 30 {
newIter := obiseq.MakeIBioSequenceBatch()
newIter := obiiter.MakeIBioSequenceBatch()
newIter.Close()
return newIter, nil
}
@ -89,10 +90,11 @@ func ReadSequencesBatchFromFile(filename string, options ...WithOption) (obiseq.
filename, filetype)
}
return obiseq.NilIBioSequenceBatch, nil
return obiiter.NilIBioSequenceBatch, nil
}
func ReadSequencesFromFile(filename string, options ...WithOption) (obiseq.IBioSequence, error) {
func ReadSequencesFromFile(filename string,
options ...WithOption) (obiiter.IBioSequence, error) {
ib, err := ReadSequencesBatchFromFile(filename, options...)
return ib.SortBatches().IBioSequence(), err