I have a tab-separated file that I think is already sorted on the first 3 columns. Here is a 2-line sample in a file named foo:
chr10 60379 60380 10:60380-60380 T/T
chr10 60379 60380 10:60380-60380 G/T
I try checking it with
sort -s -k1,1V -k2,2n -k3,3n -c foo
but the check fails:
sort: foo:2: disorder: chr10 60379 60380 10:60380-60380 G/T
If I sort it using the above key specification, it swaps the order of the lines:
sort -s -k1,1V -k2,2n -k3,3n foo
chr10 60379 60380 10:60380-60380 G/T
chr10 60379 60380 10:60380-60380 T/T
Here it is with --debug:
$ sort -s -k1,1V -k2,2n -k3,3n --debug foo
sort: using ‘en_US.UTF-8’ sorting rules
sort: leading blanks are significant in key 1; consider also specifying 'b'
chr10>60379>60380>10:60380-60380>G/T
_____
_____
_____
chr10>60379>60380>10:60380-60380>T/T
_____
_____
_____
Here is some info about what I'm running:
$ sort --version
sort (GNU coreutils) 8.22
$ more /etc/*-release
::::::::::::::
/etc/oracle-release
::::::::::::::
Oracle Linux Server release 7.1
$ uname -r
3.8.13-68.1.2.el7uek.x86_64
Many thanks for your help!
Terry
--------
Terry Farrah
Bioinformatics Scientist
Institute for Systems Biology
206-732-1348