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change the model for representing paired reads and extend its usage to other commands

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This commit is contained in:
Eric Coissac
2023-02-23 23:35:58 +01:00
parent ebb05fcdf7
commit 072b85e155
23 changed files with 598 additions and 338 deletions
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10
pkg/obioptions/options.go
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@ -11,7 +11,7 @@ import (
)
var _Debug = false
var _ParallelWorkers = runtime.NumCPU() - 1
var _ParallelWorkers = runtime.NumCPU() * 2 - 1
var _MaxAllowedCPU = runtime.NumCPU()
var _BufferSize = 1
var _BatchSize = 5000
@ -19,7 +19,10 @@ var _BatchSize = 5000
type ArgumentParser func([]string) (*getoptions.GetOpt, []string, error)
func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser {
options := getoptions.New()
options.SetMode(getoptions.Bundling)
options.SetUnknownMode(getoptions.Fail)
options.Bool("help", false, options.Alias("h", "?"))
options.BoolVar(&_Debug, "debug", false)
@ -28,6 +31,7 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
options.Description("Number of parallele threads computing the result"))
options.IntVar(&_MaxAllowedCPU, "max-cpu", _MaxAllowedCPU,
options.GetEnv("OBIMAXCPU"),
options.Description("Number of parallele threads computing the result"))
for _, o := range optionset {
@ -42,6 +46,10 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
runtime.GOMAXPROCS(_MaxAllowedCPU)
if options.Called("max-cpu") {
log.Printf("CPU number limited to %d", _MaxAllowedCPU)
if ! options.Called("workers") {
_ParallelWorkers=_MaxAllowedCPU * 2 - 1
log.Printf("Number of workers set %d", _ParallelWorkers)
}
}
if options.Called("no-singleton") {