From 9811e440b88b8f1a2a00c7ae62ad49c2a1df4edf Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Tue, 7 Mar 2023 11:06:08 +0700 Subject: [PATCH] Takes into account the option parsing errors Former-commit-id: d0b3ed0b96a72f79f887df8fbc325427e63d7a73 --- cmd/obitools/obiannotate/main.go | 2 +- cmd/obitools/obiclean/main.go | 2 +- cmd/obitools/obicleandb/main.go | 2 +- cmd/obitools/obicomplement/main.go | 2 +- cmd/obitools/obiconvert/main.go | 2 +- cmd/obitools/obicount/main.go | 2 +- cmd/obitools/obicsv/main.go | 13 +++++++++---- cmd/obitools/obidistribute/main.go | 2 +- cmd/obitools/obifind/main.go | 2 +- cmd/obitools/obigrep/main.go | 2 +- cmd/obitools/obimultiplex/main.go | 2 +- cmd/obitools/obipcr/main.go | 2 +- cmd/obitools/obirefidx/main.go | 2 +- cmd/obitools/obitag/main.go | 2 +- cmd/obitools/obiuniq/main.go | 2 +- 15 files changed, 23 insertions(+), 18 deletions(-) diff --git a/cmd/obitools/obiannotate/main.go b/cmd/obitools/obiannotate/main.go index ed45267..80e0943 100644 --- a/cmd/obitools/obiannotate/main.go +++ b/cmd/obitools/obiannotate/main.go @@ -32,7 +32,7 @@ func main() { optionParser := obioptions.GenerateOptionParser(obiannotate.OptionSet) - _, args, _ := optionParser(os.Args) + _, args := optionParser(os.Args) sequences, _ := obiconvert.CLIReadBioSequences(args...) annotator := obiannotate.CLIAnnotationPipeline() diff --git a/cmd/obitools/obiclean/main.go b/cmd/obitools/obiclean/main.go index 4216e4e..7dce48c 100644 --- a/cmd/obitools/obiclean/main.go +++ b/cmd/obitools/obiclean/main.go @@ -13,7 +13,7 @@ import ( func main() { optionParser := obioptions.GenerateOptionParser(obiclean.OptionSet) - _, args, _ := optionParser(os.Args) + _, args := optionParser(os.Args) fs, _ := obiconvert.CLIReadBioSequences(args...) diff --git a/cmd/obitools/obicleandb/main.go b/cmd/obitools/obicleandb/main.go index c69d0ef..8fdda19 100644 --- a/cmd/obitools/obicleandb/main.go +++ b/cmd/obitools/obicleandb/main.go @@ -12,7 +12,7 @@ import ( func main() { optionParser := obioptions.GenerateOptionParser(obicleandb.OptionSet) - _, args, _ := optionParser(os.Args) + _, args := optionParser(os.Args) fs, _ := obiconvert.CLIReadBioSequences(args...) diff --git a/cmd/obitools/obicomplement/main.go b/cmd/obitools/obicomplement/main.go index 476f66b..8ae1f48 100644 --- a/cmd/obitools/obicomplement/main.go +++ b/cmd/obitools/obicomplement/main.go @@ -13,7 +13,7 @@ import ( func main() { optionParser := obioptions.GenerateOptionParser(obiconvert.OptionSet) - _, args, _ := optionParser(os.Args) + _, args := optionParser(os.Args) fs, _ := obiconvert.CLIReadBioSequences(args...) diff --git a/cmd/obitools/obiconvert/main.go b/cmd/obitools/obiconvert/main.go index f53ea58..fd670e2 100644 --- a/cmd/obitools/obiconvert/main.go +++ b/cmd/obitools/obiconvert/main.go @@ -12,7 +12,7 @@ import ( func main() { optionParser := obioptions.GenerateOptionParser(obiconvert.OptionSet) - _, args, _ := optionParser(os.Args) + _, args := optionParser(os.Args) fs, _ := obiconvert.CLIReadBioSequences(args...) obiconvert.CLIWriteBioSequences(fs, true) diff --git a/cmd/obitools/obicount/main.go b/cmd/obitools/obicount/main.go index c5e1981..ba347a1 100644 --- a/cmd/obitools/obicount/main.go +++ b/cmd/obitools/obicount/main.go @@ -31,7 +31,7 @@ func main() { obicount.OptionSet, ) - _, args, _ := optionParser(os.Args) + _, args := optionParser(os.Args) fs, _ := obiconvert.CLIReadBioSequences(args...) nvariant, nread, nsymbol := fs.Count(true) diff --git a/cmd/obitools/obicsv/main.go b/cmd/obitools/obicsv/main.go index f05a730..49cfdf2 100644 --- a/cmd/obitools/obicsv/main.go +++ b/cmd/obitools/obicsv/main.go @@ -1,16 +1,21 @@ package main import ( + "os" + "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter" + "git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions" + "git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obicsv" + "git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert" ) func main() { - // optionParser := obioptions.GenerateOptionParser(obiconvert.OptionSet) + optionParser := obioptions.GenerateOptionParser(obicsv.OptionSet) - // _, args, _ := optionParser(os.Args) + _, args := optionParser(os.Args) - // fs, _ := obiconvert.ReadBioSequences(args...) - // //obicsv.CLIWriteCSV(fs, true) + fs, _ := obiconvert.CLIReadBioSequences(args...) + obicsv.CLIWriteCSV(fs, true) obiiter.WaitForLastPipe() diff --git a/cmd/obitools/obidistribute/main.go b/cmd/obitools/obidistribute/main.go index 2f2e980..b83340c 100644 --- a/cmd/obitools/obidistribute/main.go +++ b/cmd/obitools/obidistribute/main.go @@ -13,7 +13,7 @@ import ( func main() { optionParser := obioptions.GenerateOptionParser(obidistribute.OptionSet) - _, args, _ := optionParser(os.Args) + _, args := optionParser(os.Args) fs, _ := obiconvert.CLIReadBioSequences(args...) diff --git a/cmd/obitools/obifind/main.go b/cmd/obitools/obifind/main.go index 126b024..a0887c9 100644 --- a/cmd/obitools/obifind/main.go +++ b/cmd/obitools/obifind/main.go @@ -11,7 +11,7 @@ import ( func main() { optionParser := obioptions.GenerateOptionParser(obifind.OptionSet) - _, args, _ := optionParser(os.Args) + _, args := optionParser(os.Args) //prof, _ := os.Create("obifind.prof") //pprof.StartCPUProfile(prof) diff --git a/cmd/obitools/obigrep/main.go b/cmd/obitools/obigrep/main.go index 4a56310..da4c087 100644 --- a/cmd/obitools/obigrep/main.go +++ b/cmd/obitools/obigrep/main.go @@ -32,7 +32,7 @@ func main() { optionParser := obioptions.GenerateOptionParser(obigrep.OptionSet) - _, args, _ := optionParser(os.Args) + _, args := optionParser(os.Args) sequences, _ := obiconvert.CLIReadBioSequences(args...) selected := obigrep.CLIFilterSequence(sequences) diff --git a/cmd/obitools/obimultiplex/main.go b/cmd/obitools/obimultiplex/main.go index 0e6d7f1..c351e6c 100644 --- a/cmd/obitools/obimultiplex/main.go +++ b/cmd/obitools/obimultiplex/main.go @@ -27,7 +27,7 @@ func main() { optionParser := obioptions.GenerateOptionParser(obimultiplex.OptionSet) - _, args, _ := optionParser(os.Args) + _, args := optionParser(os.Args) sequences, _ := obiconvert.CLIReadBioSequences(args...) amplicons, _ := obimultiplex.IExtractBarcode(sequences) diff --git a/cmd/obitools/obipcr/main.go b/cmd/obitools/obipcr/main.go index 8e67528..45995b4 100644 --- a/cmd/obitools/obipcr/main.go +++ b/cmd/obitools/obipcr/main.go @@ -29,7 +29,7 @@ func main() { optionParser := obioptions.GenerateOptionParser(obipcr.OptionSet) - _, args, _ := optionParser(os.Args) + _, args := optionParser(os.Args) sequences, _ := obiconvert.CLIReadBioSequences(args...) amplicons, _ := obipcr.PCR(sequences) diff --git a/cmd/obitools/obirefidx/main.go b/cmd/obitools/obirefidx/main.go index a6b3988..f336363 100644 --- a/cmd/obitools/obirefidx/main.go +++ b/cmd/obitools/obirefidx/main.go @@ -13,7 +13,7 @@ import ( func main() { optionParser := obioptions.GenerateOptionParser(obirefidx.OptionSet) - _, args, _ := optionParser(os.Args) + _, args := optionParser(os.Args) fs, _ := obiconvert.CLIReadBioSequences(args...) indexed := obirefidx.IndexReferenceDB(fs) diff --git a/cmd/obitools/obitag/main.go b/cmd/obitools/obitag/main.go index 4011caf..52f6849 100644 --- a/cmd/obitools/obitag/main.go +++ b/cmd/obitools/obitag/main.go @@ -31,7 +31,7 @@ func main() { optionParser := obioptions.GenerateOptionParser(obitag.OptionSet) - _, args, _ := optionParser(os.Args) + _, args := optionParser(os.Args) fs, _ := obiconvert.CLIReadBioSequences(args...) identified := obitag.AssignTaxonomy(fs) diff --git a/cmd/obitools/obiuniq/main.go b/cmd/obitools/obiuniq/main.go index e9ef08d..9c8e2b8 100644 --- a/cmd/obitools/obiuniq/main.go +++ b/cmd/obitools/obiuniq/main.go @@ -32,7 +32,7 @@ func main() { optionParser := obioptions.GenerateOptionParser(obiuniq.OptionSet) - _, args, _ := optionParser(os.Args) + _, args := optionParser(os.Args) sequences, _ := obiconvert.CLIReadBioSequences(args...) unique := obiuniq.Unique(sequences)