Add jbrowse sort-gff subcommand

[cmdcolin]

This helps automate the sorting of a gff, which can require tedious typing

This could be used in the Current Protocols paper also as a way to reduce steps

Assumes a unix-y type system with sh, sort, grep

[cmdcolin]

Usage

jbrowse sort-gff file.gff | bgzip > out.sorted.gff.gz
tabix out.sorted.gff.gz

[codecov]

Codecov Report

Merging #4032 (e37048e) into main (4fe46f8) will increase coverage by 0.02%.
Report is 1 commits behind head on main.
The diff coverage is 33.33%.

❗ Current head e37048e differs from pull request most recent head 7924c6d. Consider uploading reports for the commit 7924c6d to get more accurate results

@@            Coverage Diff             @@
##             main    #4032      +/-   ##
==========================================
+ Coverage   63.68%   63.70%   +0.02%     
==========================================
  Files        1026     1027       +1     
  Lines       30251    30260       +9     
  Branches     7199     7201       +2     
==========================================
+ Hits        19264    19276      +12     
+ Misses      10822    10817       -5     
- Partials      165      167       +2     

Files	Coverage Δ
products/jbrowse-cli/src/commands/sort-gff.ts	33.33% <33.33%> (ø)

... and 2 files with indirect coverage changes

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[cmdcolin]

any thoughts on adding this to CLI @garrettjstevens ?

[garrettjstevens]

Yeah, looks good to me. sort does exist on Windows, but since grep does not, it should properly error out there. Also I think these commands should work on BSD sort/grep as well as GNU.

It could be worth a note in the description that this will not preserve the locations of comments or ### sync directives, although that's the same probably no matter how you sort it.

[cmdcolin]

excellent, updated description. It actually now checks for 'sh' too because it uses 'sh' to launch the subshell syntax that is being used