Colin Diesh

I would say the easiest track to reproduce this on is the BAM tracks, e.g. http://jbrowse.org/code/JBrowse-1.12.0/?data=sample_data/json/volvox&loc=ctgA:24449..34449&tracks=DNA,volvox-paired_bam Just mentioning because this is sometimes inconsistent

Apollo has the ability to do jump to next/prev feature for the special "User-created annotations" track, but it is a special case because the "User-created annotations" track downloads the entire...

There are several ways to create links to jbrowse regions or features: http://gmod.org/wiki/JBrowse_Configuration_Guide#loc You can link to regions of the browser using a format like this http://host/jbrowse/index.html?loc=chr1:100..2000 Alternatively you can...

This feature was brought up again by @malcook yesterday as a way of quickly trying to flip through regions of interest

this also is only applied to IndexNames e.g. generate-names...is it something that needs distributing more widely? more reading on filetest here https://perldoc.perl.org/filetest

I also wonder: what was the error before this change was added? Was it unable to write things it should have been able to write to?

seems like this should be ok. it does say in the docs here https://perldoc.perl.org/filetest to consider this carefully, but if it helps and doesn't have side effects then it seems...

Are you referring to chromosome features in the GFF (like a single line that has column three type being chromosome)? Why is there a mixture of Chr1 and chr1 in...

I think the current behavior makes sense, and I imagine in the case where no Name is specified, that it just makes ID == Name. It seems in this case...

note that if you really wanted to also, you could also put the alternative name as an Alias in the gff, and in that case generate-names will index that alternative...