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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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26
pkg/obiformats/universal_write.go
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@ -6,10 +6,10 @@ import (
"log"
"os"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
)
func WriteSequences(iterator obiseq.IBioSequence,
func WriteSequences(iterator obiiter.IBioSequence,
file io.Writer,
options ...WithOption) error {
@ -34,7 +34,7 @@ func WriteSequences(iterator obiseq.IBioSequence,
return nil
}
func WriteSequencesToFile(iterator obiseq.IBioSequence,
func WriteSequencesToFile(iterator obiiter.IBioSequence,
filename string,
options ...WithOption) error {
@ -48,13 +48,13 @@ func WriteSequencesToFile(iterator obiseq.IBioSequence,
return WriteSequences(iterator, file, options...)
}
func WriteSequencesToStdout(iterator obiseq.IBioSequence, options ...WithOption) error {
func WriteSequencesToStdout(iterator obiiter.IBioSequence, options ...WithOption) error {
return WriteSequences(iterator, os.Stdout, options...)
}
func WriteSequenceBatch(iterator obiseq.IBioSequenceBatch,
func WriteSequenceBatch(iterator obiiter.IBioSequenceBatch,
file io.Writer,
options ...WithOption) (obiseq.IBioSequenceBatch, error) {
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
iterator = iterator.Rebatch(1000)
@ -64,7 +64,7 @@ func WriteSequenceBatch(iterator obiseq.IBioSequenceBatch,
batch := iterator.Get()
iterator.PushBack()
var newIter obiseq.IBioSequenceBatch
var newIter obiiter.IBioSequenceBatch
var err error
if len(batch.Slice()) > 0 {
@ -84,24 +84,24 @@ func WriteSequenceBatch(iterator obiseq.IBioSequenceBatch,
return iterator, nil
}
return obiseq.NilIBioSequenceBatch, fmt.Errorf("input iterator not ready")
return obiiter.NilIBioSequenceBatch, fmt.Errorf("input iterator not ready")
}
func WriteSequencesBatchToStdout(iterator obiseq.IBioSequenceBatch,
options ...WithOption) (obiseq.IBioSequenceBatch, error) {
func WriteSequencesBatchToStdout(iterator obiiter.IBioSequenceBatch,
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
options = append(options, OptionDontCloseFile())
return WriteSequenceBatch(iterator, os.Stdout, options...)
}
func WriteSequencesBatchToFile(iterator obiseq.IBioSequenceBatch,
func WriteSequencesBatchToFile(iterator obiiter.IBioSequenceBatch,
filename string,
options ...WithOption) (obiseq.IBioSequenceBatch, error) {
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
file, err := os.Create(filename)
if err != nil {
log.Fatalf("open file error: %v", err)
return obiseq.NilIBioSequenceBatch, err
return obiiter.NilIBioSequenceBatch, err
}
options = append(options, OptionCloseFile())