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Change the memory management for thee BuildAlignment function

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This commit is contained in:
Eric Coissac
2022-01-15 19:10:16 +01:00
parent e8fff6477b
commit e1b7e1761c
11 changed files with 145 additions and 1329 deletions
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16
pkg/obiformats/universal_write.go
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@ -54,7 +54,7 @@ func WriteSequencesToStdout(iterator obiseq.IBioSequence, options ...WithOption)
func WriteSequenceBatch(iterator obiseq.IBioSequenceBatch,
file io.Writer,
options ...WithOption) (obiseq.IBioSequenceBatch,error) {
options ...WithOption) (obiseq.IBioSequenceBatch, error) {
var newIter obiseq.IBioSequenceBatch
var err error
@ -65,25 +65,25 @@ func WriteSequenceBatch(iterator obiseq.IBioSequenceBatch,
iterator.PushBack()
batch := iterator.Get()
if batch.Slice()[0].HasQualities() {
newIter,err = WriteFastqBatch(iterator, file, options...)
newIter, err = WriteFastqBatch(iterator, file, options...)
} else {
newIter,err = WriteFastaBatch(iterator, file, options...)
newIter, err = WriteFastaBatch(iterator, file, options...)
}
return newIter,err
return newIter, err
}
return obiseq.NilIBioSequenceBatch,fmt.Errorf("input iterator not ready")
return obiseq.NilIBioSequenceBatch, fmt.Errorf("input iterator not ready")
}
func WriteSequencesBatchToStdout(iterator obiseq.IBioSequenceBatch,
options ...WithOption) (obiseq.IBioSequenceBatch,error) {
func WriteSequencesBatchToStdout(iterator obiseq.IBioSequenceBatch,
options ...WithOption) (obiseq.IBioSequenceBatch, error) {
return WriteSequenceBatch(iterator, os.Stdout, options...)
}
func WriteSequencesBatchToFile(iterator obiseq.IBioSequenceBatch,
filename string,
options ...WithOption) (obiseq.IBioSequenceBatch,error) {
options ...WithOption) (obiseq.IBioSequenceBatch, error) {
file, err := os.Create(filename)