Shore sort

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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