View source for Shore idtrans

SHORE uses numerical identifiers for all sequences of the reference.
'''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).

Required is either a ''*.trans'' file which is stored in the ''[[IndexFolder]]'' by ''shore preprocess'', or a ''ref.txt'' file generated by ''shore mapflowcell''.


'''Usage:''' shore idtrans [OPTIONS] FILES

{|
 | colspan=2 | '''Allowed options'''
 |----
 | ''-t'', ''--transfile=<arg>''      ||                     || *.trans file from ''[[IndexFolder]]''
 |----
 | ''-r'', ''--reffile=<arg>''        ||                     || ref.txt file generated by mapflowcell
 |----
 | ''-o'', ''--outfile=<arg>''        ||                     || Output file (default: <infile>.idtrans)
 |----
 | ''-c'', ''--columns=<arg[,...]>''  || (Default: ''chr'')  || Columns to be translated (column names or @<column_number>)
 |----
 | ''--name2id''                      ||                     || Translate names to IDs (default: translate IDs to names)
 |----
 | ''--nocompress''                   ||                     || Do not compress output files
 |----
 |}