Get column names from BED tabix files and other utils for external jbrowse-plugin-gwas support

[cmdcolin]

This adds a "linear manhattan plot display"

Also makes it so that stats are available on the base adapter, so that means that all the different adapters types that use some basic stats (which includes, SNPCoverageAdapter, BigWigAdapter, GCCoverageAdapter (#1624), and now BEDTabix for manhattan plot) all don't have to individually implement stats

This is similar to jbrowse 1 where the base seqfeature store has a local stats operation

Then it also adds ability for BedTabixAdapter to choose it's "score column" and read column names from the header of the bedtabix file if available

This allows us to choose the column named "neg_log_pvalue" in the summary_stats.txt.gz file as the score that is plotted with the manhattan plot from a tabix file prepared from summary_stats.txt.gz from here https://my.locuszoom.org/gwas/236887/

Can display whole-genome-wide results and local results

[codecov]

Codecov Report

Merging #1630 (cd7be9b) into master (708bafa) will increase coverage by 0.01%.
The diff coverage is 84.37%.

@@            Coverage Diff             @@
##           master    #1630      +/-   ##
==========================================
+ Coverage   58.90%   58.92%   +0.01%     
==========================================
  Files         446      446              
  Lines       20467    20493      +26     
  Branches     4824     4834      +10     
==========================================
+ Hits        12057    12076      +19     
- Misses       8112     8119       +7     
  Partials      298      298              

Impacted Files	Coverage Δ
plugins/bed/src/BedTabixAdapter/BedTabixAdapter.ts	88.23% <83.33%> (-4.79%)	⬇️
...gle/src/LinearWiggleDisplay/components/Tooltip.tsx	40.00% <100.00%> (ø)
plugins/wiggle/src/index.ts	100.00% <100.00%> (ø)
...inearGenomeView/components/RefNameAutocomplete.tsx	89.36% <0.00%> (-4.26%)	⬇️

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[cmdcolin]

There are some potential add ons to this that could include

1. Making this a custom track type, otherwise it is part of featuretrack and runs into confusion trying to be solved by Add new menu items for show/hide feature labels, set max height, and set compact display mode #1394
2. Adding some informative mouseover for the dots, might not be necessary to get the point across though

[cmdcolin]

Random observation: the manhattan plot on the my.locuszoom.org page is rendered with SVG using binned data, so each X coordinate is a line and a circle at the top instead of millions of circles. Apparently, it's also server side rendered, so you don't see any accessing the data file and only a small amount of rendered svg is downloaded over the wire to view that plot. It's still relatively slow to view that same track whole genome in this branch but there are probably some optimizations, and it is also possible to zoom in on jbrowse 2 which is important...

[cmdcolin]

Rebased onto #1640

[cmdcolin]

This PR sort of has a couple options to go forward

1. This GWAS module splits off into an external plugin. This has challenges because the gwas plugin uses a fair amount of stuff from @jbrowse/plugin-wiggle. So, either it adds a NPM dependency to @jbrowse/plugin-wiggle, which could go stale, or we copy and paste the wiggle stuff into the external GWAS plugin so it is more self sufficient, or we figure out a way to share plugin resources with our reexports?
2. We accept it as is and improve it in the core repo

[garrettjstevens]

or we figure out a way to share plugin resources with our reexports

You can do this with exports on the plugin class. There's an example of the GDC plugin using LGV plugin resources here: https://github.com/GMOD/jbrowse-plugin-gdc/blob/c6d89158a0b4fa955f42eb68da01c04cb68540e1/src/index.ts#L27-L30

[cmdcolin]

thanks, that is quite interesting

I found that if I tried to add a proper @jbrowse/plugin-wiggle to my devdeps I got some very weird errors even trying to run yarn

ed by node_modules/@gmod/binary-parser/dist/binary_parser.js, but could not be resolved – treating it as an external dependency
'fs' is imported by node_modules/canvas/index.js, but could not be resolved – treating it as an external dependency
'fs' is imported by node_modules/canvas/index.js, but could not be resolved – treating it as an external dependency
'zlib' is imported by node_modules/@gmod/bbi/dist/blockView.js, but could not be resolved – treating it as an external dependency
'zlib' is imported by node_modules/@gmod/bbi/dist/blockView.js, but could not be resolved – treating it as an external dependency
'fs' is imported by fs?commonjs-external, but could not be resolved – treating it as an external dependency
'zlib' is imported by zlib?commonjs-external, but could not be resolved – treating it as an external dependency
'vm' is imported by vm?commonjs-external, but could not be resolved – treating it as an external dependency
'fs' is imported by fs?commonjs-external, but could not be resolved – treating it as an external dependency
'zlib' is imported by zlib?commonjs-external, but could not be resolved – treating it as an external dependency
'vm' is imported by vm?commonjs-external, but could not be resolved – treating it as an external dError: Unexpected character '' (Note that you need plugins to import files that are not JavaScript)

at /home/cdiesh/src/jbrowse-plugin-gwas2/node_modules/canvas/build/Release/canvas.node:1:0

1: ELF>0W@@�@8@  p�p�$p����$$P�td�V�V�V

Q�tdGNU���SBw��u���K|����@
                            �@"�"
   ^
2: @D0� @Ā���� �@       (�@��D)�!�      ��@"��@H@҂���d  @Hp �(%
3: J` ! F���PL`����P
                    � ���

I may have to forego the typescripting on @jbrowse/plugin-wiggle and not have it in devdeps since that would be all that gains me

[cmdcolin]

I'll just modify this PR to erase core plugins/gwas from history
Seems a little esoteric and plugins can be a bit more agile sometimes

[garrettjstevens]

I found that if I tried to add a proper @jbrowse/plugin-wiggle to my devdeps I got some very weird errors even trying to run yarn

I get that error when doing a top-level import of @jbrowse/plugin-wiggle, but if I don't do a top-level import and use the ... as import('@jbrowse/plugin-wiggle') syntax it seems to be fine.

[cmdcolin]

awesome thanks for checking that out

[cmdcolin]

Alright, I ripped the gwas plugin out into an external plugin, thanks very much @garrettjstevens for the tips

If this remaining PR is merged then it would provide features that support to that plugin namely

1. wiggle re-exports that @garrettjstevens mentioned
2. BEDTabix header parsing
3. choosing a "score" column from the BEDTabix header
4. Actually using the column numbers specified in the tabix header for the BEDTabix instead of assuming 1,2,3 are chr,start,end

https://github.com/cmdcolin/jbrowse-plugin-gwas

[cmdcolin]

Tested and the plugin does work if using this branch