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Adds possibility to provide the ngsfilter configuration as a CSV file

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Former-commit-id: f0fd2cb1a7b149ae2a330edc5087b21be2c4585b
This commit is contained in:
Eric Coissac
2024-05-31 11:08:20 +02:00
parent dbeb44bc79
commit 4487723d14
4 changed files with 160 additions and 12 deletions
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16
pkg/obioptions/options.go
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@ -21,8 +21,8 @@ var _ParallelFilesRead = 0
var _MaxAllowedCPU = runtime.NumCPU()
var _BatchSize = 5000
var _Pprof = false
var _Quality_Shift_Input = 33
var _Quality_Shift_Output = 33
var _Quality_Shift_Input = byte(33)
var _Quality_Shift_Output = byte(33)
var _Version = "4.2.1"
type ArgumentParser func([]string) (*getoptions.GetOpt, []string)
@ -266,7 +266,7 @@ func SetBatchSize(n int) {
//
// No parameters.
// Returns an integer representing the quality shift value for input.
func InputQualityShift() int {
func InputQualityShift() byte {
return _Quality_Shift_Input
}
@ -274,22 +274,22 @@ func InputQualityShift() int {
//
// No parameters.
// Returns an integer representing the quality shift value for output.
func OutputQualityShift() int {
func OutputQualityShift() byte {
return _Quality_Shift_Output
}
// SetInputQualityShift sets the quality shift value for decoding FASTQ.
//
// n - an integer representing the quality shift value to be set.
func SetInputQualityShift(n int) {
_Quality_Shift_Input = n
func SetInputQualityShift[T int | byte](n T) {
_Quality_Shift_Input = byte(n)
}
// SetOutputQualityShift sets the quality shift value used for FASTQ output.
//
// n - an integer representing the quality shift value to be set.
func SetOutputQualityShift(n int) {
_Quality_Shift_Output = n
func SetOutputQualityShift[T int | byte](n T) {
_Quality_Shift_Output = byte(n)
}
// SetMaxCPU sets the maximum number of CPU cores allowed.