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Refactoring of the default values

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This commit is contained in:
Eric Coissac
2025-01-24 18:09:59 +01:00
parent 3137c1f841
commit 9acb4a85a8
50 changed files with 337 additions and 166 deletions
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51
pkg/obioptions/options.go
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@ -6,6 +6,7 @@ import (
"os"
"runtime"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitaxformat"
log "github.com/sirupsen/logrus"
@ -28,9 +29,6 @@ var _BatchSize = 2000
var _Pprof = false
var _PprofMudex = 10
var _PprofGoroutine = 6060
var _Quality_Shift_Input = byte(33)
var _Quality_Shift_Output = byte(33)
var _Read_Qualities = true
var __taxonomy__ = ""
var __alternative_name__ = false
@ -177,7 +175,7 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
// }
if options.Called("solexa") {
SetInputQualityShift(64)
obidefault.SetReadQualitiesShift(64)
}
return options, remaining
@ -292,10 +290,6 @@ func CLIBatchSize() int {
return _BatchSize
}
func CLIReadQualities() bool {
return _Read_Qualities
}
// SetDebugOn sets the debug mode on.
func SetDebugOn() {
_Debug = true
@ -306,10 +300,6 @@ func SetDebugOff() {
_Debug = false
}
func SetReadQualities(status bool) {
_Read_Qualities = status
}
// SetWorkerPerCore sets the number of workers per CPU core.
//
// It takes a float64 parameter representing the number of workers
@ -359,43 +349,6 @@ func SetBatchSize(n int) {
_BatchSize = n
}
// InputQualityShift returns the quality shift value for input.
//
// It can be set programmatically by the SetInputQualityShift() function.
// This value is used to decode the quality scores in FASTQ files.
// The quality shift value defaults to 33, which is the correct value for
// Sanger formated FASTQ files.
// The quality shift value can be modified to 64 by the command line option
// --solexa, for decoding old Solexa formated FASTQ files.
//
// No parameters.
// Returns an integer representing the quality shift value for input.
func InputQualityShift() byte {
return _Quality_Shift_Input
}
// OutputQualityShift returns the quality shift value used for FASTQ output.
//
// No parameters.
// Returns an integer representing the quality shift value for output.
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[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[T int | byte](n T) {
_Quality_Shift_Output = byte(n)
}
// SetMaxCPU sets the maximum number of CPU cores allowed.
//
// n - an integer representing the new maximum number of CPU cores.