obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

Refactoring

Browse Source
This commit is contained in:
Eric Coissac
2022-01-14 15:16:41 +01:00
parent 69c61bc190
commit 3848c54184
5 changed files with 10 additions and 10 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
cmd/obitools/obiconvert/main.go
View File

@ -9,9 +9,9 @@ import (
) )
func main() { func main() {
option_parser := obioptions.GenerateOptionParser(obiconvert.OptionSet) optionParser := obioptions.GenerateOptionParser(obiconvert.OptionSet)
_, args, _ := option_parser(os.Args) _, args, _ := optionParser(os.Args)
fs, _ := obiconvert.ReadBioSequences(args...) fs, _ := obiconvert.ReadBioSequences(args...)
obiconvert.WriteBioSequences(fs) obiconvert.WriteBioSequences(fs)

4
cmd/obitools/obicount/main.go
View File

@ -28,12 +28,12 @@ func main() {
trace.Start(ftrace) trace.Start(ftrace)
defer trace.Stop() defer trace.Stop()
option_parser := obioptions.GenerateOptionParser( optionParser := obioptions.GenerateOptionParser(
obiconvert.InputOptionSet, obiconvert.InputOptionSet,
obicount.OptionSet, obicount.OptionSet,
) )
_, args, _ := option_parser(os.Args) _, args, _ := optionParser(os.Args)
fs, _ := obiconvert.ReadBioSequences(args...) fs, _ := obiconvert.ReadBioSequences(args...)
nread := 0 nread := 0

4
cmd/obitools/obifind/main.go
View File

@ -9,9 +9,9 @@ import (
) )
func main() { func main() {
option_parser := obioptions.GenerateOptionParser(obifind.OptionSet) optionParser := obioptions.GenerateOptionParser(obifind.OptionSet)
_, args, _ := option_parser(os.Args) _, args, _ := optionParser(os.Args)
//prof, _ := os.Create("obifind.prof") //prof, _ := os.Create("obifind.prof")
//pprof.StartCPUProfile(prof) //pprof.StartCPUProfile(prof)

4
cmd/obitools/obipairing/main.go
View File

@ -28,9 +28,9 @@ func main() {
// trace.Start(ftrace) // trace.Start(ftrace)
// defer trace.Stop() // defer trace.Stop()
option_parser := obioptions.GenerateOptionParser(obipairing.OptionSet) optionParser := obioptions.GenerateOptionParser(obipairing.OptionSet)
option_parser(os.Args) optionParser(os.Args)
pairs, _ := obipairing.IBatchPairedSequence() pairs, _ := obipairing.IBatchPairedSequence()
paired := obipairing.IAssemblePESequencesBatch(pairs, 2, 50, 20, true) paired := obipairing.IAssemblePESequencesBatch(pairs, 2, 50, 20, true)
written, _ := obiformats.WriteFastqBatchToStdout(paired) written, _ := obiformats.WriteFastqBatchToStdout(paired)

4
cmd/obitools/obipcr/main.go
View File

@ -24,9 +24,9 @@ func main() {
// trace.Start(ftrace) // trace.Start(ftrace)
// defer trace.Stop() // defer trace.Stop()
option_parser := obioptions.GenerateOptionParser(obipcr.OptionSet) optionParser := obioptions.GenerateOptionParser(obipcr.OptionSet)
_, args, _ := option_parser(os.Args) _, args, _ := optionParser(os.Args)
sequences, _ := obiconvert.ReadBioSequencesBatch(args...) sequences, _ := obiconvert.ReadBioSequencesBatch(args...)
amplicons, _ := obipcr.PCR(sequences) amplicons, _ := obipcr.PCR(sequences)