First commit

pkg/obiformats/options.go

@@ -0,0 +1,158 @@
+package obiformats
+
+import "git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+
+type __options__ struct {
+	fastseq_header_parser obiseq.SeqAnnotator
+	fastseq_header_writer func(obiseq.BioSequence) string
+	with_progress_bar     bool
+	buffer_size           int
+	batch_size            int
+	quality_shift         int
+	parallel_workers      int
+}
+
+type Options struct {
+	pointer *__options__
+}
+
+type WithOption func(Options)
+
+func MakeOptions(setters []WithOption) Options {
+	o := __options__{
+		fastseq_header_parser: ParseGuessedFastSeqHeader,
+		fastseq_header_writer: FormatFastSeqJsonHeader,
+		with_progress_bar:     false,
+		buffer_size:           2,
+		quality_shift:         33,
+		parallel_workers:      4,
+		batch_size:            5000,
+	}
+
+	opt := Options{&o}
+
+	for _, set := range setters {
+		set(opt)
+	}
+
+	return opt
+}
+
+func (opt Options) QualityShift() int {
+	return opt.pointer.quality_shift
+}
+
+func (opt Options) BufferSize() int {
+	return opt.pointer.buffer_size
+}
+
+func (opt Options) BatchSize() int {
+	return opt.pointer.batch_size
+}
+
+func (opt Options) ParallelWorkers() int {
+	return opt.pointer.parallel_workers
+}
+
+func (opt Options) ParseFastSeqHeader() obiseq.SeqAnnotator {
+	return opt.pointer.fastseq_header_parser
+}
+
+func (opt Options) FormatFastSeqHeader() func(obiseq.BioSequence) string {
+	return opt.pointer.fastseq_header_writer
+}
+
+func (opt Options) ProgressBar() bool {
+	return opt.pointer.with_progress_bar
+}
+
+func OptionsBufferSize(size int) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.buffer_size = size
+	})
+
+	return f
+}
+
+// Allows to specify the ascii code corresponding to
+// a quality of 0 in fastq encoded quality scores.
+func OptionsQualityShift(shift int) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.quality_shift = shift
+	})
+
+	return f
+}
+
+// Allows to specify a quality shift of 33, corresponding
+// to a FastQ file qualities encoded following Sanger
+// convention. This corresponds to Illumina produced FastQ
+// files.
+func OptionsQualitySanger() WithOption {
+	return OptionsQualityShift(33)
+}
+
+// Allows to specify a quality shift of 64, corresponding
+// to a FastQ file qualities encoded following the Solexa
+// convention.
+func OptionsQualitySolexa() WithOption {
+	return OptionsQualityShift(64)
+}
+
+func OptionsFastSeqHeaderParser(parser obiseq.SeqAnnotator) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.fastseq_header_parser = parser
+	})
+
+	return f
+}
+
+func OptionFastSeqDoNotParseHeader() WithOption {
+	return OptionsFastSeqHeaderParser(nil)
+}
+
+func OptionsFastSeqDefaultHeaderParser() WithOption {
+	return OptionsFastSeqHeaderParser(ParseGuessedFastSeqHeader)
+}
+
+// OptionsFastSeqHeaderFormat allows foor specifying the format
+// used to write FASTA and FASTQ sequence.
+func OptionsFastSeqHeaderFormat(format func(obiseq.BioSequence) string) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.fastseq_header_writer = format
+	})
+
+	return f
+}
+
+func OptionsParallelWorkers(nworkers int) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.parallel_workers = nworkers
+	})
+
+	return f
+}
+
+func OptionsBatchSize(size int) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.batch_size = size
+	})
+
+	return f
+}
+
+func OptionsWithProgressBar() WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.with_progress_bar = true
+	})
+
+	return f
+}
+
+func OptionsWithoutProgressBar() WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.with_progress_bar = false
+	})
+
+	return f
+}