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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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1
pkg/obitools/obimultiplex/demultiplex.go
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@@ -16,6 +16,7 @@ func IExtractBarcode(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error
opts = append(opts,
obingslibrary.OptionAllowedMismatches(CLIAllowedMismatch()),
obingslibrary.OptionAllowedIndel(CLIAllowsIndel()),
obingslibrary.OptionUnidentified(CLIUnidentifiedFileName()),
obingslibrary.OptionDiscardErrors(!CLIConservedErrors()),
obingslibrary.OptionParallelWorkers(obioptions.CLIParallelWorkers()),

7
pkg/obitools/obimultiplex/options.go
View File

@@ -13,6 +13,7 @@ import (
var _NGSFilterFile = ""
var _UnidentifiedFile = ""
var _AllowedMismatch = int(2)
var _AllowsIndel = false
var _ConservedError = false
// PCROptionSet defines every options related to a simulated PCR.
@@ -33,6 +34,9 @@ func MultiplexOptionSet(options *getoptions.GetOpt) {
options.BoolVar(&_ConservedError, "keep-errors", _ConservedError,
options.Description("Prints symbol counts."))
options.BoolVar(&_AllowsIndel, "with-indels", _AllowsIndel,
options.Description("Allows for indels during the primers matching."))
options.StringVar(&_UnidentifiedFile, "unidentified", _UnidentifiedFile,
options.Alias("u"),
options.Description("Filename used to store the sequences unassigned to any sample."))
@@ -52,6 +56,9 @@ func CLIAllowedMismatch() int {
return _AllowedMismatch
}
func CLIAllowsIndel() bool {
return _AllowsIndel
}
func CLIUnidentifiedFileName() string {
return _UnidentifiedFile
}

4
pkg/obitools/obipcr/options.go
View File

@@ -59,7 +59,7 @@ func OptionSet(options *getoptions.GetOpt) {
// ForwardPrimer returns the sequence of the forward primer as indicated by the
// --forward command line option
func ForwardPrimer() string {
pattern, err := obiapat.MakeApatPattern(_ForwardPrimer, _AllowedMismatch)
pattern, err := obiapat.MakeApatPattern(_ForwardPrimer, _AllowedMismatch, false)
if err != nil {
log.Fatalf("%+v", err)
@@ -73,7 +73,7 @@ func ForwardPrimer() string {
// ReversePrimer returns the sequence of the reverse primer as indicated by the
// --reverse command line option
func ReversePrimer() string {
pattern, err := obiapat.MakeApatPattern(_ReversePrimer, _AllowedMismatch)
pattern, err := obiapat.MakeApatPattern(_ReversePrimer, _AllowedMismatch,false)
if err != nil {
log.Fatalf("%+v", err)