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Add the possibility to look for patterns allowing indels.

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Former-commit-id: 0599c2b0ad16df086dbdb08e491503870d8904be
This commit is contained in:
Eric Coissac
2023-03-20 15:28:24 +07:00
parent 5fbe52368c
commit 27d6c60e25
14 changed files with 674 additions and 219 deletions
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18
pkg/obingslibrary/worker.go
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@ -8,6 +8,7 @@ type _Options struct {
discardErrors bool
unidentified string
allowedMismatch int
allowsIndel bool
withProgressBar bool
parallelWorkers int
batchSize int
@ -55,6 +56,14 @@ func OptionAllowedMismatches(count int) WithOption {
return f
}
func OptionAllowedIndel(allowed bool) WithOption {
f := WithOption(func(opt Options) {
opt.pointer.allowsIndel = allowed
})
return f
}
// OptionParallelWorkers sets how many search
// jobs will be run in parallel.
func OptionParallelWorkers(nworkers int) WithOption {
@ -87,6 +96,10 @@ func (options Options) AllowedMismatch() int {
return options.pointer.allowedMismatch
}
func (options Options) AllowsIndel() bool {
return options.pointer.allowsIndel
}
func (options Options) WithProgressBar() bool {
return options.pointer.withProgressBar
}
@ -110,6 +123,7 @@ func MakeOptions(setters []WithOption) Options {
discardErrors: true,
unidentified: "",
allowedMismatch: 0,
allowsIndel: false,
withProgressBar: false,
parallelWorkers: 4,
batchSize: 1000,
@ -145,7 +159,7 @@ func ExtractBarcodeSlice(ngslibrary NGSLibrary,
opt := MakeOptions(options)
ngslibrary.Compile(opt.AllowedMismatch())
ngslibrary.Compile(opt.AllowedMismatch(),opt.AllowsIndel())
return _ExtractBarcodeSlice(ngslibrary, sequences, opt)
}
@ -155,7 +169,7 @@ func ExtractBarcodeSliceWorker(ngslibrary NGSLibrary,
opt := MakeOptions(options)
ngslibrary.Compile(opt.AllowedMismatch())
ngslibrary.Compile(opt.AllowedMismatch(),opt.AllowsIndel())
worker := func(sequences obiseq.BioSequenceSlice) obiseq.BioSequenceSlice {
return _ExtractBarcodeSlice(ngslibrary, sequences, opt)