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add the --skip-empty option

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Former-commit-id: ec9cb0ecaf90a61bf9289cf4c089b5cc2fcb65a5
This commit is contained in:
Eric Coissac
2023-07-17 14:24:02 +02:00
parent b44fcfb2a0
commit be47ec909c
10 changed files with 65 additions and 12 deletions
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2
pkg/obitools/obiclean/obiclean.go
View File

@@ -285,7 +285,7 @@ func Weight(sequence *obiseq.BioSequence) map[string]int {
return weight
}
func IOBIClean(itertator obiiter.IBioSequence) obiiter.IBioSequence {
func CLIOBIClean(itertator obiiter.IBioSequence) obiiter.IBioSequence {
db := itertator.Load()

8
pkg/obitools/obiconvert/options.go
View File

@@ -26,6 +26,7 @@ var __output_solexa_quality__ = false
var __no_progress_bar__ = false
var __compressed__ = false
var __skip_empty__ = false
var __output_file_name__ = "-"
var __paired_file_name__ = ""
@@ -70,6 +71,9 @@ func OutputModeOptionSet(options *getoptions.GetOpt) {
options.Alias("Z"),
options.Description("Output is compressed"))
options.BoolVar(&__skip_empty__, "skip-empty", __skip_empty__,
options.Description("Sequences of length equal to zero are suppressed from the output"))
options.StringVar(&__output_file_name__, "out", __output_file_name__,
options.Alias("o"),
options.ArgName("FILENAME"),
@@ -141,6 +145,10 @@ func CLICompressed() bool {
return __compressed__
}
func CLISkipEmpty() bool {
return __skip_empty__
}
func CLIInputFastHeaderFormat() string {
switch {
case __input_fastjson_format__:

4
pkg/obitools/obiconvert/sequence_writer.go
View File

@@ -80,6 +80,8 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
var reverse string
fn, reverse = BuildPairedFileNames(fn)
opts = append(opts, obiformats.WritePairedReadsTo(reverse))
} else {
opts = append(opts, obiformats.OptionsSkipEmptySequence(CLISkipEmpty()))
}
switch CLIOutputFormat() {
@@ -91,6 +93,7 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
newIter, err = obiformats.WriteSequencesToFile(iterator, fn, opts...)
}
} else {
opts = append(opts, obiformats.OptionsSkipEmptySequence(CLISkipEmpty()))
switch CLIOutputFormat() {
case "fastq":
newIter, err = obiformats.WriteFastqToStdout(iterator, opts...)
@@ -99,6 +102,7 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
default:
newIter, err = obiformats.WriteSequencesToStdout(iterator, opts...)
}
}
if err != nil {