mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-06-24 17:51:00 +00:00
Eric Coissac
60 lines
1.3 KiB
Go
60 lines
1.3 KiB
Go
package main
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import (
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"fmt"
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"os"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicount"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
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)
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func main() {
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// f, err := os.Create("cpu.pprof")
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// if err != nil {
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// log.Fatal(err)
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// }
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// pprof.StartCPUProfile(f)
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// defer pprof.StopCPUProfile()
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// ftrace, err := os.Create("cpu.trace")
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// if err != nil {
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// log.Fatal(err)
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// }
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// trace.Start(ftrace)
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// defer trace.Stop()
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optionParser := obioptions.GenerateOptionParser(
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"obicount",
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"counts the sequences present in a file of sequences",
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obiconvert.InputOptionSet,
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obicount.OptionSet,
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)
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_, args := optionParser(os.Args)
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obidefault.SetStrictReadWorker(min(4, obidefault.ParallelWorkers()))
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fs, err := obiconvert.CLIReadBioSequences(args...)
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obiconvert.OpenSequenceDataErrorMessage(args, err)
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nvariant, nread, nsymbol := fs.Count(true)
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fmt.Print("entities,n\n")
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if obicount.CLIIsPrintingVariantCount() {
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fmt.Printf("variants,%d\n", nvariant)
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}
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if obicount.CLIIsPrintingReadCount() {
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fmt.Printf("reads,%d\n", nread)
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}
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if obicount.CLIIsPrintingSymbolCount() {
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fmt.Printf("symbols,%d\n", nsymbol)
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}
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}
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