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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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18
pkg/obitools/obiconvert/sequence_reader.go
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@ -7,8 +7,8 @@ import (
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
func _ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
@ -66,9 +66,9 @@ func _ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
return list_of_files, nil
}
func ReadBioSequencesBatch(filenames ...string) (obiseq.IBioSequenceBatch, error) {
var iterator obiseq.IBioSequenceBatch
var reader func(string, ...obiformats.WithOption) (obiseq.IBioSequenceBatch, error)
func ReadBioSequencesBatch(filenames ...string) (obiiter.IBioSequenceBatch, error) {
var iterator obiiter.IBioSequenceBatch
var reader func(string, ...obiformats.WithOption) (obiiter.IBioSequenceBatch, error)
opts := make([]obiformats.WithOption, 0, 10)
@ -106,7 +106,7 @@ func ReadBioSequencesBatch(filenames ...string) (obiseq.IBioSequenceBatch, error
list_of_files, err := _ExpandListOfFiles(false, filenames...)
if err != nil {
return obiseq.NilIBioSequenceBatch, err
return obiiter.NilIBioSequenceBatch, err
}
switch InputFormat() {
@ -121,16 +121,16 @@ func ReadBioSequencesBatch(filenames ...string) (obiseq.IBioSequenceBatch, error
iterator, err = reader(list_of_files[0], opts...)
if err != nil {
return obiseq.NilIBioSequenceBatch, err
return obiiter.NilIBioSequenceBatch, err
}
list_of_files = list_of_files[1:]
others := make([]obiseq.IBioSequenceBatch, 0, len(list_of_files))
others := make([]obiiter.IBioSequenceBatch, 0, len(list_of_files))
for _, fn := range list_of_files {
r, err := reader(fn, opts...)
if err != nil {
return obiseq.NilIBioSequenceBatch, err
return obiiter.NilIBioSequenceBatch, err
}
others = append(others, r)
}
@ -152,7 +152,7 @@ func ReadBioSequencesBatch(filenames ...string) (obiseq.IBioSequenceBatch, error
return iterator, nil
}
func ReadBioSequences(filenames ...string) (obiseq.IBioSequence, error) {
func ReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
ib, err := ReadBioSequencesBatch(filenames...)
return ib.SortBatches().IBioSequence(), err