Shore sort
From SHORE wiki
shore sort sorts, merges or queries tab-delimited text files.
Command line options
Usage: shore sort [OPTIONS] [TEXT_FILES]
| Allowed options | ||
| -i, --infiles=<arg[,...]> | A comma-separated list of plain-text input files | |
| -o, --outfile=<arg> | (Default: stdout) | Output file |
| -p, --preset=<arg> | Automatically select sort keys for the file type specified. Supported values: * maplist: map.list format sorted by genomic coordinate * maplist_id: map.list format sorted by read ID * reads0: reads flat file format sorted by read ID * gff: GFF format sorted by position | |
| -k, --keystring=<arg> | Concatenation of column ids (counted from 1) and key types. Valid key types: t (text), i (integer) and f (float); capital letters reverse the sort order - e.g. '-k 1i5t3i7I'. | |
| -I, --inplace | Output file is the same as the input file | |
| -t, --tmpdir=<arg> | Temporary file directory (defaults to $TMPDIR or /tmp) | |
| -B, --blocksize=<arg> | (Default: 2048) | Block size in megabytes |
| -m, --nur-merge | Merge already sorted files | |
| -u, --unique | Output only the first of an equal run | |
| -c, --check | Only test if the files are sorted | |
| -b, --upper-bound=<arg[,...]> | Returns byte offset (counted from 0) and text of the first line in a sorted file that compares greater than the keys given in <arg> (provide comma-separated values in order of key priority) | |
| -T, --tail=<arg[,...]> | Print all lines in a sorted file that compare greater than the keys given in <arg> (provide comma-separated values in order of key priority) | |
| -C, --no-comments | Do not treat line comments and empty lines specially | |
| -v, --verbose | Be more verbose | |
