wga bam files in Jbrowse config

[adf-ncgr]

currently, the populate-jbrowse handles adding the paf files from genome_alignments but doesn't seem to add tracks for the associated bam files. Although the two files contain similar data, JBrowse2 only uses indexing with respect to the bam files, meaning that they are much faster to load when just looking at a linear genome view. So, I think we ought to make both available as tracks.

[adf-ncgr]

seems like this isn't quite working. The error I get suggests that it is trying to assign the same track id to both the track representing the paf file and the one representing the bam file (which probably is because it is stripping off the .bam and .paf.gz suffixes to generate a track id). So, probably we'll have to explicitly set the track id for at least on of these. Maybe just using the filename without stripping off suffixes is as sensible as anything else I could imagine doing. For the record here's the full error:

 ›   Error: Cannot add track with id
 ›   arahy.Tifrunner.gnm2.x.aradu.V14167.gnm2.DWM1, a track with that id
 ›   already exists (use --force to override)
Traceback (most recent call last):
  File "/home/legumista/lis_autocontent_env/bin/lis-autocontent", line 33, in <module>
    sys.exit(load_entry_point('lis-autocontent==0.0.4', 'console_scripts', 'lis-autocontent')())
  File "/home/legumista/lis_autocontent_env/lib64/python3.10/site-packages/lis_autocontent-0.0.4-py3.10.egg/EGG-INFO/scripts/lis_autocontent.py", line 19, in cli_entry_point
  File "/home/legumista/lis_autocontent_env/lib64/python3.10/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/home/legumista/lis_autocontent_env/lib64/python3.10/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/home/legumista/lis_autocontent_env/lib64/python3.10/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/legumista/lis_autocontent_env/lib64/python3.10/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/legumista/lis_autocontent_env/lib64/python3.10/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/home/legumista/lis_autocontent_env/lib64/python3.10/site-packages/lis_autocontent-0.0.4-py3.10.egg/EGG-INFO/scripts/lis_cli.py", line 157, in populate_jbrowse2
  File "/home/legumista/lis_autocontent_env/lib64/python3.10/site-packages/lis_autocontent-0.0.4-py3.10.egg/EGG-INFO/scripts/process_collections.py", line 204, in populate_jbrowse2
  File "/home/legumista/lis_autocontent_env/lib64/python3.10/site-packages/lis_autocontent-0.0.4-py3.10.egg/EGG-INFO/scripts/process_collections.py", line 194, in process_collections
  File "/usr/lib64/python3.10/subprocess.py", line 369, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'jbrowse add-track --assemblyNames aradu.V14167.gnm2,arahy.Tifrunner.gnm2 --out test/ https://data.legumeinfo.org/Arachis/hypogaea/genome_alignments/Tifrunner.gnm2.wga.DWM1/arahy.Tifrunner.gnm2.x.aradu.V14167.gnm2.DWM1.paf.gz --force;jbrowse add-track -a arahy.Tifrunner.gnm2 --indexFile https://data.legumeinfo.org/Arachis/hypogaea/genome_alignments/Tifrunner.gnm2.wga.DWM1/arahy.Tifrunner.gnm2.x.aradu.V14167.gnm2.DWM1.bam.bai https://data.legumeinfo.org/Arachis/hypogaea/genome_alignments/Tifrunner.gnm2.wga.DWM1/arahy.Tifrunner.gnm2.x.aradu.V14167.gnm2.DWM1.bam' returned non-zero exit status 160.

[adf-ncgr]

@ctcncgr this is now technically working, although I'd like to see some further changes. At the moment the name/ids for a given comparison are as reported here:

Overwrote track with name "aradu.V14167.gnm2.x.araip.K30076.gnm2.96TT.paf" and trackId "aradu.V14167.gnm2.x.araip.K30076.gnm2.96TT.paf" in test//config.json
Overwrote track with name "araip.K30076.gnm2xaradu.V14167.gnm2 BAM" and trackId "aradu.V14167.gnm2.x.araip.K30076.gnm2.96TT" in ./config.json

One problem seen in the above is that the bam is getting written to ./config.json while the paf is getting written to test/config.json; the latter is correct, given that I had specified --jbrowse_out test

Another problem (somewhat cosmetic) is that the name for the bam track switches the order of the two genomes in the comparison (ie araip is coming first) and the separator should be ".x." not just "x". Also, I think for consistency we ought to just have the name end with ".bam" instead of " BAM" and the trackId should also have ".bam" added (similar to how the other one is using ".paf" in both these contexts).

I'll comment on dotplot stuff over on #28

[ctcncgr]

@adf-ncgr I think I fixed the naming inconsistencies and changed the order of the refs in the BAM.

[adf-ncgr]

almost there, I think you just need to also add the .bam to the end of the trackId for the bam tracks; still coming out as the unsuffixed file name:
Overwrote track with name "aradu.V14167.gnm2.x.arast.V10309.gnm1.96TT.bam" and trackId "**aradu.V14167.gnm2.x.arast.V10309.gnm1.96TT**" in /var/www/html/jbrowse-web-v2.3.4/arachis/test//config.json

[ctcncgr]

@adf-ncgr ok this should now set the trackId correctly.

[adf-ncgr]

yes, I think it's good now, thanks