diff --git a/cmd/test/main.go b/cmd/test/main.go index 219c713..f6a64fe 100644 --- a/cmd/test/main.go +++ b/cmd/test/main.go @@ -1,38 +1,35 @@ package main import ( - "os" + "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obifp" + "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obikmer" + "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq" log "github.com/sirupsen/logrus" - - "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter" - "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert" - - "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions" ) func main() { - optionParser := obioptions.GenerateOptionParser(obiconvert.OptionSet) - _, args := optionParser(os.Args) + one := obifp.OneUint[obifp.Uint128]() + a, b := obifp.OneUint[obifp.Uint64]().LeftShift64(66, 0) + log.Infof("one: %v, %v", a, b) + shift := one.LeftShift(66) + log.Infof("one: %v", shift) - fs, err := obiconvert.CLIReadBioSequences(args...) + seq := obiseq.NewBioSequence("test", []byte("atcgggttccaacc"), "") - if err != nil { - log.Errorf("Cannot open file (%v)", err) - os.Exit(1) - } - - frags := obiiter.IFragments( - 1000, - 100, - 10, - 100, - obioptions.CLIParallelWorkers(), + kmermap := obikmer.NewKmerMap[obifp.Uint128]( + obiseq.BioSequenceSlice{ + seq, + }, + 7, + true, ) - obiconvert.CLIWriteBioSequences(fs.Pipe(frags), true) + kmers := kmermap.NormalizedKmerSlice(seq, nil) - obiiter.WaitForLastPipe() + for _, kmer := range kmers { + println(kmermap.KmerAsString(kmer)) + } } diff --git a/pkg/obioptions/version.go b/pkg/obioptions/version.go index d111bc8..956df64 100644 --- a/pkg/obioptions/version.go +++ b/pkg/obioptions/version.go @@ -7,7 +7,7 @@ import ( // TODO: The version number is extracted from git. This induces that the version // corresponds to the last commit, and not the one when the file will be // commited -var _Commit = "05bf2bf" +var _Commit = "b37fc39" var _Version = "Release 4.2.0" // Version returns the version of the obitools package.