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Add an option alowwing to use the pool method instead of the concat method when several input files are specified

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This commit is contained in:
Eric Coissac
2022-08-21 13:43:00 +02:00
parent 844e24b818
commit 34e957d3fb
1 changed files with 18 additions and 7 deletions
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25
pkg/obitools/obiconvert/options.go
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@ -7,6 +7,8 @@ import (
var __skipped_entries__ = 0
var __read_only_entries__ = -1
var __no_ordered_input__ = false
var __input_fastjson_format__ = false
var __input_fastobi_format__ = false
@ -22,26 +24,30 @@ var __output_fastobi_format__ = false
var __output_solexa_quality__ = false
func InputOptionSet(options *getoptions.GetOpt) {
options.IntVar(&__skipped_entries__, "skip", 0,
options.IntVar(&__skipped_entries__, "skip", __skipped_entries__,
options.Description("The N first sequence records of the file are discarded from the analysis and not reported to the output file."))
options.IntVar(&__read_only_entries__, "only", -1,
options.IntVar(&__read_only_entries__, "only", __read_only_entries__,
options.Description("Only the N next sequence records of the file are analyzed. The following sequences in the file are neither analyzed, neither reported to the output file. This option can be used conjointly with the –skip option."))
options.BoolVar(&__input_fastjson_format__, "input-json-header", false,
options.BoolVar(&__input_fastjson_format__, "input-json-header", __input_fastjson_format__,
options.Description("FASTA/FASTQ title line annotations follow json format."))
options.BoolVar(&__input_fastobi_format__, "input-OBI-header", false,
options.BoolVar(&__input_fastobi_format__, "input-OBI-header", __input_fastobi_format__,
options.Description("FASTA/FASTQ title line annotations follow OBI format."))
options.BoolVar(&__input_ecopcr_format__, "ecopcr", false,
options.BoolVar(&__input_ecopcr_format__, "ecopcr", __input_ecopcr_format__,
options.Description("Read data following the ecoPCR output format."))
options.BoolVar(&__input_embl_format__, "embl", false,
options.BoolVar(&__input_embl_format__, "embl", __input_embl_format__,
options.Description("Read data following the EMBL flatfile format."))
options.BoolVar(&__input_solexa_quality__, "solexa", false,
options.BoolVar(&__input_solexa_quality__, "solexa", __input_solexa_quality__,
options.Description("Decodes quality string according to the Solexa specification."))
options.BoolVar(&__no_ordered_input__, "no-order", __no_ordered_input__,
options.Description("When several imput files are provided, "+
"indicates that there is no order among them."))
}
func OutputOptionSet(options *getoptions.GetOpt) {
@ -79,6 +85,11 @@ func InputFormat() string {
}
}
// Returns true if the order among several imput files has not to be considered
func NoInputOrder() bool {
return __no_ordered_input__
}
func OutputFormat() string {
switch {
case __output_in_fastq__: