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Work on EMBL and Genbank parser efficienct

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Former-commit-id: 309cc9ce4eea4c8085d7d4451a66a81710532f07
This commit is contained in:
Eric Coissac
2024-02-20 13:23:07 +01:00
parent 95caebec8f
commit 1542ce4c63
4 changed files with 69 additions and 14 deletions
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28
pkg/obiformats/options.go
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@ -11,6 +11,7 @@ type __options__ struct {
with_progress_bar bool
buffer_size int
batch_size int
total_seq_size int
full_file_batch bool
parallel_workers int
closefile bool
@ -29,6 +30,7 @@ type __options__ struct {
csv_auto bool
paired_filename string
source string
with_feature_table bool
}
type Options struct {
@ -45,6 +47,7 @@ func MakeOptions(setters []WithOption) Options {
buffer_size: 2,
parallel_workers: obioptions.CLIReadParallelWorkers(),
batch_size: obioptions.CLIBatchSize(),
total_seq_size: 1024 * 1024 * 100, // 100 MB by default
full_file_batch: false,
closefile: false,
appendfile: false,
@ -62,6 +65,7 @@ func MakeOptions(setters []WithOption) Options {
csv_auto: false,
paired_filename: "",
source: "",
with_feature_table: false,
}
opt := Options{&o}
@ -77,6 +81,10 @@ func (opt Options) BatchSize() int {
return opt.pointer.batch_size
}
func (opt Options) TotalSeqSize() int {
return opt.pointer.total_seq_size
}
func (opt Options) FullFileBatch() bool {
return opt.pointer.full_file_batch
}
@ -169,6 +177,10 @@ func (opt Options) Source() string {
return opt.pointer.source
}
func (opt Options) WithFeatureTable() bool {
return opt.pointer.with_feature_table
}
func OptionCloseFile() WithOption {
f := WithOption(func(opt Options) {
opt.pointer.closefile = true
@ -259,6 +271,14 @@ func OptionsBatchSize(size int) WithOption {
return f
}
func OptionsBatchSizeDefault(bp int) WithOption {
f := WithOption(func(opt Options) {
opt.pointer.batch_size = bp
})
return f
}
func OptionsFullFileBatch(full bool) WithOption {
f := WithOption(func(opt Options) {
opt.pointer.full_file_batch = full
@ -386,3 +406,11 @@ func CSVAutoColumn(auto bool) WithOption {
return f
}
func WithFeatureTable(with bool) WithOption {
f := WithOption(func(opt Options) {
opt.pointer.with_feature_table = with
})
return f
}