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Patch for some lost of data during sequence writing

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This commit is contained in:
Eric Coissac
2023-02-08 13:14:26 +01:00
parent 4117cbdd08
commit 526bf79c7f
16 changed files with 99 additions and 10 deletions
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4
cmd/obitools/obiannotate/main.go
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@ -3,6 +3,7 @@ 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/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiannotate"
@ -36,4 +37,7 @@ func main() {
sequences, _ := obiconvert.ReadBioSequences(args...)
annotator := obiannotate.CLIAnnotationPipeline()
obiconvert.WriteBioSequences(sequences.Pipe(annotator), true)
obiiter.WaitForLastPipe()
}

4
cmd/obitools/obiclean/main.go
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@ -3,6 +3,7 @@ package main
import (
"os"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiclean"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
@ -19,4 +20,7 @@ func main() {
cleaned := obiclean.IOBIClean(fs)
obiconvert.WriteBioSequences(cleaned, true)
obiiter.WaitForLastPipe()
}

4
cmd/obitools/obicomplement/main.go
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@ -3,6 +3,7 @@ package main
import (
"os"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
@ -18,4 +19,7 @@ func main() {
comp := fs.MakeIWorker(obiseq.ReverseComplementWorker(true))
obiconvert.WriteBioSequences(comp, true)
obiiter.WaitForLastPipe()
}

4
cmd/obitools/obiconvert/main.go
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@ -3,6 +3,7 @@ package main
import (
"os"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
@ -15,4 +16,7 @@ func main() {
fs, _ := obiconvert.ReadBioSequences(args...)
obiconvert.WriteBioSequences(fs, true)
obiiter.WaitForLastPipe()
}

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

@ -3,6 +3,7 @@ package main
import (
"os"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obidistribute"
@ -16,4 +17,7 @@ func main() {
fs, _ := obiconvert.ReadBioSequences(args...)
obidistribute.DistributeSequence(fs)
obiiter.WaitForLastPipe()
}

3
cmd/obitools/obigrep/main.go
View File

@ -3,6 +3,7 @@ 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/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
@ -36,4 +37,6 @@ func main() {
sequences, _ := obiconvert.ReadBioSequences(args...)
selected := obigrep.IFilterSequence(sequences)
obiconvert.WriteBioSequences(selected, true)
obiiter.WaitForLastPipe()
}

3
cmd/obitools/obimultiplex/main.go
View File

@ -3,6 +3,7 @@ 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/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obimultiplex"
@ -32,4 +33,6 @@ func main() {
amplicons, _ := obimultiplex.IExtractBarcode(sequences)
obiconvert.WriteBioSequences(amplicons, true)
amplicons.Wait()
obiiter.WaitForLastPipe()
}

3
cmd/obitools/obipairing/main.go
View File

@ -3,6 +3,7 @@ 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/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obipairing"
@ -39,4 +40,6 @@ func main() {
obioptions.CLIParallelWorkers(),
)
obiconvert.WriteBioSequences(paired, true)
obiiter.WaitForLastPipe()
}

3
cmd/obitools/obipcr/main.go
View File

@ -3,6 +3,7 @@ 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/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obipcr"
@ -33,4 +34,6 @@ func main() {
sequences, _ := obiconvert.ReadBioSequences(args...)
amplicons, _ := obipcr.PCR(sequences)
obiconvert.WriteBioSequences(amplicons, true)
obiiter.WaitForLastPipe()
}

6
cmd/obitools/obirefidx/main.go
View File

@ -3,6 +3,7 @@ package main
import (
"os"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obirefidx"
@ -17,6 +18,7 @@ func main() {
fs, _ := obiconvert.ReadBioSequences(args...)
indexed := obirefidx.IndexReferenceDB(fs)
written, _ := obiconvert.WriteBioSequences(indexed, false)
written.Consume()
obiconvert.WriteBioSequences(indexed, true)
obiiter.WaitForLastPipe()
}

2
cmd/obitools/obitag/main.go
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@ -4,6 +4,7 @@ import (
"fmt"
"os"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obitag"
@ -36,6 +37,7 @@ func main() {
identified := obitag.AssignTaxonomy(fs)
obiconvert.WriteBioSequences(identified, true)
obiiter.WaitForLastPipe()
fmt.Println("")
}

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

@ -3,6 +3,7 @@ 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/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
@ -36,4 +37,7 @@ func main() {
sequences, _ := obiconvert.ReadBioSequences(args...)
unique := obiuniq.Unique(sequences)
obiconvert.WriteBioSequences(unique, true)
obiiter.WaitForLastPipe()
}