Difference between revisions of "Shore 2dex"
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(Created page with ''''shore 2dex''' implements range-indexed queries for tab-delimited text files. '''Usage:''' shore 2dex [OPTIONS] [TEXT_FILES] {| | colspan=2 | '''Mandatory''' |---- | ''-i…') |
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implements range-indexed queries for tab-delimited text files. | implements range-indexed queries for tab-delimited text files. | ||
| + | ==Command line options== | ||
'''Usage:''' shore 2dex [OPTIONS] [TEXT_FILES] | '''Usage:''' shore 2dex [OPTIONS] [TEXT_FILES] | ||
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| colspan=2 | '''Mandatory''' | | colspan=2 | '''Mandatory''' | ||
|---- | |---- | ||
| − | | ''-i'', ''--infiles=<arg[,...]>'' || || A comma-separated list of tab-delimited plain-text input files (can also be any [[ | + | | ''-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) |
|---- | |---- | ||
|---- | |---- | ||
Latest revision as of 10:12, 27 September 2011
shore 2dex implements range-indexed queries for tab-delimited text files.
Command line options
Usage: shore 2dex [OPTIONS] [TEXT_FILES]
| 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) | |
| 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 | |
| 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 |
| 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) | |
| Other | ||
| -v, --verbose | Be more verbose | |
| -Q, --quiet | Be less verbose | |
