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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/fastseq_write_fastq.go
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@ -8,6 +8,7 @@ import (
"os"
"time"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
@ -34,7 +35,7 @@ func FormatFastq(seq *obiseq.BioSequence, quality_shift int, formater FormatHead
)
}
func FormatFastqBatch(batch obiseq.BioSequenceBatch, quality_shift int,
func FormatFastqBatch(batch obiiter.BioSequenceBatch, quality_shift int,
formater FormatHeader) []byte {
var bs bytes.Buffer
for _, seq := range batch.Slice() {
@ -44,7 +45,7 @@ func FormatFastqBatch(batch obiseq.BioSequenceBatch, quality_shift int,
return bs.Bytes()
}
func WriteFastq(iterator obiseq.IBioSequence, file io.Writer, options ...WithOption) error {
func WriteFastq(iterator obiiter.IBioSequence, file io.Writer, options ...WithOption) error {
opt := MakeOptions(options)
header_format := opt.FormatFastSeqHeader()
@ -65,7 +66,7 @@ func WriteFastq(iterator obiseq.IBioSequence, file io.Writer, options ...WithOpt
return nil
}
func WriteFastqToFile(iterator obiseq.IBioSequence,
func WriteFastqToFile(iterator obiiter.IBioSequence,
filename string,
options ...WithOption) error {
@ -80,7 +81,7 @@ func WriteFastqToFile(iterator obiseq.IBioSequence,
return WriteFastq(iterator, file, options...)
}
func WriteFastqToStdout(iterator obiseq.IBioSequence, options ...WithOption) error {
func WriteFastqToStdout(iterator obiiter.IBioSequence, options ...WithOption) error {
options = append(options, OptionDontCloseFile())
return WriteFastq(iterator, os.Stdout, options...)
}
@ -90,11 +91,13 @@ type FileChunck struct {
order int
}
func WriteFastqBatch(iterator obiseq.IBioSequenceBatch, file io.Writer, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
func WriteFastqBatch(iterator obiiter.IBioSequenceBatch,
file io.Writer,
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
opt := MakeOptions(options)
buffsize := iterator.BufferSize()
newIter := obiseq.MakeIBioSequenceBatch(buffsize)
newIter := obiiter.MakeIBioSequenceBatch(buffsize)
nwriters := opt.ParallelWorkers()
@ -113,7 +116,7 @@ func WriteFastqBatch(iterator obiseq.IBioSequenceBatch, file io.Writer, options
close(chunkchan)
}()
ff := func(iterator obiseq.IBioSequenceBatch) {
ff := func(iterator obiiter.IBioSequenceBatch) {
for iterator.Next() {
batch := iterator.Get()
chunk := FileChunck{
@ -165,20 +168,21 @@ func WriteFastqBatch(iterator obiseq.IBioSequenceBatch, file io.Writer, options
return newIter, nil
}
func WriteFastqBatchToStdout(iterator obiseq.IBioSequenceBatch, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
func WriteFastqBatchToStdout(iterator obiiter.IBioSequenceBatch,
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
options = append(options, OptionDontCloseFile())
return WriteFastqBatch(iterator, os.Stdout, options...)
}
func WriteFastqBatchToFile(iterator obiseq.IBioSequenceBatch,
func WriteFastqBatchToFile(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())