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add an option alias -O for the old obi format

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This commit is contained in:
Eric Coissac
2022-02-24 07:26:55 +01:00
parent f5b278f5ec
commit f18cc034bb
5 changed files with 44 additions and 93 deletions
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1
pkg/obitools/obiconvert/options.go
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@ -54,6 +54,7 @@ func OutputOptionSet(options *getoptions.GetOpt) {
options.BoolVar(&__output_fastjson_format__, "output-json-header", false,
options.Description("output FASTA/FASTQ title line annotations follow json format."))
options.BoolVar(&__output_fastobi_format__, "output-OBI-header", false,
options.Alias("O"),
options.Description("output FASTA/FASTQ title line annotations follow OBI format."))
options.BoolVar(&__output_solexa_quality__, "solexa-output", false,

1
pkg/obitools/obipairing/options.go
View File

@ -29,7 +29,6 @@ func PairingOptionSet(options *getoptions.GetOpt) {
options.Alias("D"),
options.Description("Length added to the fast detected overlap for the precise alignement"))
options.IntVar(&_MinOverlap, "min-overlap", _MinOverlap,
options.Alias("O"),
options.Description("Minimum ovelap between both the reads to consider the aligment"))
options.Float64Var(&_MinIdentity, "min-identity", _MinIdentity,
options.Alias("X"),