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| − | =shore idtrans=
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| − | SHORE uses numerical identifiers for all sequences of the reference.
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| − | ''shore idtrans'' simplifies translating these numbers in some of the result files back into chromosome names as specified in the reference fasta file (and vice versa).
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| − | Required is either a ''*.trans'' file which is stored in the ''[[IndexFolder]]'' by ''shore preprocess'', or a ''ref.txt'' file generated by ''shore mapflowcell''.
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| − | '''Usage:''' shore idtrans [OPTIONS] FILES
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| − | {|
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| − | | colspan=2 | '''Allowed options'''
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| − | |----
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| − | | ''-t'', ''--transfile=<arg>'' || || *.trans file from ''[[IndexFolder]]''
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| − | |----
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| − | | ''-r'', ''--reffile=<arg>'' || || ref.txt file generated by mapflowcell
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| − | |----
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| − | | ''-o'', ''--outfile=<arg>'' || || Output file (default: <infile>.idtrans)
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| − | |----
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| − | | ''-c'', ''--columns=<arg[,...]>'' || (Default: ''chr'') || Columns to be translated (column names or @<column_number>)
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| − | |----
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| − | | ''--name2id'' || || Translate names to IDs (default: translate IDs to names)
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| − | |----
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| − | | ''--nocompress'' || || Do not compress output files
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| − | |----
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| − | |}
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