obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

rename the iterator class

Browse Source
This commit is contained in:
Eric Coissac
2023-01-22 22:04:17 +01:00
parent 4592855095
commit f97f92df72
37 changed files with 399 additions and 354 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
pkg/obiformats/embl_read.go
View File

@ -84,7 +84,7 @@ func _EndOfLastEntry(buff []byte) int {
return -1
}
func _ParseEmblFile(input <-chan _FileChunk, out obiiter.IBioSequenceBatch) {
func _ParseEmblFile(input <-chan _FileChunk, out obiiter.IBioSequence) {
for chunks := range input {
scanner := bufio.NewScanner(chunks.raw)
@ -201,11 +201,11 @@ func _ReadFlatFileChunk(reader io.Reader, readers chan _FileChunk) {
// 6 5 43 2 1
//
// <CR>?<LF>//<CR>?<LF>
func ReadEMBL(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch {
func ReadEMBL(reader io.Reader, options ...WithOption) obiiter.IBioSequence {
opt := MakeOptions(options)
entry_channel := make(chan _FileChunk, opt.BufferSize())
newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize())
newIter := obiiter.MakeIBioSequence(opt.BufferSize())
nworkers := opt.ParallelWorkers()
newIter.Add(nworkers)
@ -224,7 +224,7 @@ func ReadEMBL(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch
return newIter
}
func ReadEMBLFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) {
func ReadEMBLFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
var reader io.Reader
var greader io.Reader
var err error
@ -232,7 +232,7 @@ func ReadEMBLFromFile(filename string, options ...WithOption) (obiiter.IBioSeque
reader, err = os.Open(filename)
if err != nil {
log.Printf("open file error: %+v", err)
return obiiter.NilIBioSequenceBatch, err
return obiiter.NilIBioSequence, err
}
// Test if the flux is compressed by gzip