View source for Shore 2dex

'''shore 2dex'''
implements range-indexed queries for tab-delimited text files.

==Command line options==

'''Usage:''' shore 2dex [OPTIONS] [TEXT_FILES]

{|
 | colspan=2 | '''Mandatory'''
 |----
 | ''-i'', ''--infiles=<arg[,...]>''  ||                        || A comma-separated list of tab-delimited plain-text input files (can also be any [[shore directory]] when ''-f MAPLIST'' is set)
 |----
 |----
 | colspan=2 | '''Format Options'''
 |----
 | ''-f'', ''--format=<arg>''         ||                        || Provide file type for automatic settings, valid file types: MAPLIST, GFF, SAM
 |----
 | ''-c'', ''--chr-column=<arg>''     ||                        || Column w. chromosome or sequence name, provide the column name or @<column_number>
 |----
 | ''-p'', ''--pos-column=<arg>''     ||                        || Column w. start position, provide the column name or @<column_number>
 |----
 | ''-s'', ''--size-column=<arg>''    ||                        || Column w. feature size, provide the column name or @<column_number>
 |----
 | ''-e'', ''--end-column=<arg>''     ||                        || Column w. end position (inclusive), provide the column name or @<column_number>
 |----
 | ''-x'', ''--xend-column=<arg>''    ||                        || Column w. end position (exclusive), provide the column name or @<column_number>
 |----
 | ''-C'', ''--commentchar=<arg>''    ||                        || Comment line symbol
 |----
 |----
 | colspan=2 | '''Index Options'''
 |----
 | ''-B'', ''--blocksize=<arg>''      || (Default: ''131072'')  || Block size determining the index resolution in bytes
 |----
 | ''-G'', ''--maxgap=<arg>''         || (Default: ''131072'')  || Maximum sequence gap in a block
 |----
 |----
 | colspan=2 | '''Query Options'''
 |----
 | ''-q'', ''--query=<arg>''          ||                        || A range to query; prints all overlapping records. Valid ranges: 'SEQ:POS~SIZE', 'SEQ:POS..END', 'SEQ1:POS..SEQ2:END', 'SEQ:POS...XEND', 'SEQ1:POS...SEQ2:XEND' (END: inclusive, XEND: exclusive)
 |----
 |----
 | colspan=2 | '''Other'''
 |----
 | ''-v'', ''--verbose''              ||                        || Be more verbose
 |----
 | ''-Q'', ''--quiet''                ||                        || Be less verbose
 |----
 |}