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Add some code refactoring from the blackboard branch

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This commit is contained in:
Eric Coissac
2024-08-02 12:35:46 +02:00
parent bc1aaaf7d9
commit 1b1cd41fd3
38 changed files with 491 additions and 330 deletions
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18
pkg/obiformats/options.go
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@ -7,7 +7,8 @@ import (
type __options__ struct {
fastseq_header_parser obiseq.SeqAnnotator
fastseq_header_writer func(*obiseq.BioSequence) string
fastseq_header_writer BioSequenceFormater
seqBatchFormater FormatSeqBatch
with_progress_bar bool
buffer_size int
batch_size int
@ -44,6 +45,7 @@ func MakeOptions(setters []WithOption) Options {
o := __options__{
fastseq_header_parser: ParseGuessedFastSeqHeader,
fastseq_header_writer: FormatFastSeqJsonHeader,
seqBatchFormater: nil,
with_progress_bar: false,
buffer_size: 2,
parallel_workers: obioptions.CLIReadParallelWorkers(),
@ -103,6 +105,10 @@ func (opt Options) FormatFastSeqHeader() func(*obiseq.BioSequence) string {
return opt.pointer.fastseq_header_writer
}
func (opt Options) SequenceFormater() FormatSeqBatch {
return opt.pointer.seqBatchFormater
}
func (opt Options) NoOrder() bool {
return opt.pointer.no_order
}
@ -219,8 +225,6 @@ func OptionNoOrder(no_order bool) WithOption {
return f
}
func OptionsCompressed(compressed bool) WithOption {
f := WithOption(func(opt Options) {
opt.pointer.compressed = compressed
@ -271,6 +275,14 @@ func OptionsFastSeqHeaderFormat(format func(*obiseq.BioSequence) string) WithOpt
return f
}
func OptionsSequenceFormater(formater FormatSeqBatch) WithOption {
f := WithOption(func(opt Options) {
opt.pointer.seqBatchFormater = formater
})
return f
}
func OptionsParallelWorkers(nworkers int) WithOption {
f := WithOption(func(opt Options) {
opt.pointer.parallel_workers = nworkers