Adds the command obimultiplex

pkg/obingslibrary/worker.go

@@ -0,0 +1,182 @@
+package obingslibrary
+
+import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+
+type _Options struct {
+	discardErrors   bool
+	unidentified    string
+	allowedMismatch int
+	withProgressBar bool
+	parallelWorkers int
+	batchSize       int
+	bufferSize      int
+}
+
+// Options stores a set of option usable by the
+// PCR simulation algotithm.
+type Options struct {
+	pointer *_Options
+}
+
+// WithOption is the standard type for function
+// declaring options.
+type WithOption func(Options)
+
+func OptionDiscardErrors(yes bool) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.discardErrors = yes
+	})
+
+	return f
+}
+
+func OptionUnidentified(filename string) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.unidentified = filename
+	})
+
+	return f
+}
+
+func OptionWithProgressBar(yes bool) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.withProgressBar = yes
+	})
+
+	return f
+}
+
+func OptionAllowedMismatches(count int) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.allowedMismatch = count
+	})
+
+	return f
+}
+
+// OptionBufferSize sets the requested channel
+// buffer size.
+func OptionBufferSize(size int) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.bufferSize = size
+	})
+
+	return f
+}
+
+// OptionParallelWorkers sets how many search
+// jobs will be run in parallel.
+func OptionParallelWorkers(nworkers int) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.parallelWorkers = nworkers
+	})
+
+	return f
+}
+
+// OptionBatchSize sets the requested sequence
+// batch size.
+func OptionBatchSize(size int) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.batchSize = size
+	})
+
+	return f
+}
+
+func (options Options) DiscardErrors() bool {
+	return options.pointer.unidentified == "" || options.pointer.discardErrors
+}
+
+func (options Options) Unidentified() string {
+	return options.pointer.unidentified
+}
+
+func (options Options) AllowedMismatch() int {
+	return options.pointer.allowedMismatch
+}
+
+func (options Options) WithProgressBar() bool {
+	return options.pointer.withProgressBar
+}
+
+// BufferSize returns the size of the channel
+// buffer specified by the options
+func (options Options) BufferSize() int {
+	return options.pointer.bufferSize
+}
+
+// BatchSize returns the size of the
+// sequence batch used by the PCR algorithm
+func (options Options) BatchSize() int {
+	return options.pointer.batchSize
+}
+
+// ParallelWorkers returns how many search
+// jobs will be run in parallel.
+func (options Options) ParallelWorkers() int {
+	return options.pointer.parallelWorkers
+}
+
+// MakeOptions buils a new default option set for
+// the PCR simulation algoithm.
+func MakeOptions(setters []WithOption) Options {
+	o := _Options{
+		discardErrors:   true,
+		unidentified:    "",
+		allowedMismatch: 0,
+		withProgressBar: false,
+		parallelWorkers: 4,
+		batchSize:       1000,
+		bufferSize:      100,
+	}
+
+	opt := Options{&o}
+
+	for _, set := range setters {
+		set(opt)
+	}
+
+	return opt
+}
+
+func _ExtractBarcodeSlice(ngslibrary NGSLibrary,
+	sequences obiseq.BioSequenceSlice,
+	options Options) obiseq.BioSequenceSlice {
+	newSlice := make(obiseq.BioSequenceSlice,0,len(sequences))
+	
+	for _, seq := range sequences {
+		s, err := ngslibrary.ExtractBarcode(seq,true)
+		if err==nil || ! options.pointer.discardErrors {
+			newSlice = append(newSlice, s)
+		}
+	}
+
+	return newSlice
+}
+
+func ExtractBarcodeSlice(ngslibrary NGSLibrary,
+	sequences obiseq.BioSequenceSlice,
+	options ...WithOption) obiseq.BioSequenceSlice {
+
+	opt := MakeOptions(options)
+
+	ngslibrary.Compile(opt.AllowedMismatch())
+
+	return _ExtractBarcodeSlice(ngslibrary, sequences, opt)
+}
+
+func ExtractBarcodeSliceWorker(ngslibrary NGSLibrary,
+	options ...WithOption) obiseq.SeqSliceWorker {
+
+	opt := MakeOptions(options)
+
+	ngslibrary.Compile(opt.AllowedMismatch())
+
+	worker := func(sequences obiseq.BioSequenceSlice) obiseq.BioSequenceSlice {
+		return _ExtractBarcodeSlice(ngslibrary, sequences, opt)
+	}
+
+	return worker
+}
+