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Refactoring related to iterators

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This commit is contained in:
Eric Coissac
2022-11-16 17:13:03 +01:00
parent 6f853da9df
commit 09fc426b67
29 changed files with 95 additions and 93 deletions
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10
pkg/obiformats/universal_read.go
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@ -42,7 +42,7 @@ func GuessSeqFileType(firstline string) string {
}
}
func ReadSequencesBatchFromFile(filename string,
func ReadSequencesFromFile(filename string,
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
var file *os.File
var reader io.Reader
@ -85,14 +85,14 @@ func ReadSequencesBatchFromFile(filename string,
switch filetype {
case "fastq", "fasta":
file.Close()
is, _ := ReadFastSeqBatchFromFile(filename, options...)
is, _ := ReadFastSeqFromFile(filename, options...)
return is, nil
case "ecopcr":
return ReadEcoPCRBatch(reader, options...), nil
return ReadEcoPCR(reader, options...), nil
case "embl":
return ReadEMBLBatch(reader, options...), nil
return ReadEMBL(reader, options...), nil
case "genbank":
return ReadGenbankBatch(reader, options...), nil
return ReadGenbank(reader, options...), nil
default:
log.Fatalf("File %s has guessed format %s which is not yet implemented",
filename, filetype)