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First functional version of a blackboard and a blackboard based obicount

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This commit is contained in:
Eric Coissac
2024-07-31 23:16:45 +02:00
parent dfe2fc3d43
commit f36b39bfa3
40 changed files with 1236 additions and 257 deletions
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24
cmd/obitools/obicount/main.go
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@ -4,8 +4,7 @@ import (
"fmt"
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiblackboard"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicount"
@ -35,26 +34,27 @@ func main() {
_, args := optionParser(os.Args)
obioptions.SetStrictReadWorker(min(4, obioptions.CLIParallelWorkers()))
fs, err := obiconvert.CLIReadBioSequences(args...)
black := obiblackboard.NewBlackBoard(obioptions.CLIParallelWorkers())
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
black.ReadSequences(args)
nvariant, nread, nsymbol := fs.Count(true)
counter := obiblackboard.CountSequenceAggregator("to_delete")
black.RegisterRunner("sequences", counter.Runner)
black.RegisterRunner("to_delete", obiblackboard.RecycleSequences(true, "final"))
black.Run()
if obicount.CLIIsPrintingVariantCount() {
fmt.Printf(" %d", nvariant)
fmt.Printf(" %d", counter.Variants)
}
if obicount.CLIIsPrintingReadCount() {
fmt.Printf(" %d", nread)
fmt.Printf(" %d", counter.Reads)
}
if obicount.CLIIsPrintingSymbolCount() {
fmt.Printf(" %d", nsymbol)
fmt.Printf(" %d", counter.Nucleotides)
}
fmt.Printf("\n")