Colin Diesh

Seems like this is necessary still, should it be merged?

Actually cannot even keep the useWorkspaces flag without getting some error, lerna errors out with message ``` $ lerna run useDist --scope "@jbrowse/plugin*" --scope @jbrowse/text-indexing lerna notice cli v7.1.1 lerna...

I guess to be clear, the thing that I was seeing is that minimap was running on "minimap /tmp/output.fa /tmp/output.fa" and crashing. I guess from the code it looks more...

The dojo-webpack-plugin https://github.com/OpenNTF/dojo-webpack-plugin has been pretty useful in our use cases on https://github.com/GMOD/jbrowse and it allows babel-ificiation and stuff Welcome to look at our code or the dojo-webpack-plugin has a...

it is great to hear the positive response :) i can definitely see myself running it on other ontologies now, I can look at https://github.com/obophenotype/human-phenotype-ontology/blob/master/src/ontology/hp-edit.owl I would be happy to...

great work on this! can the app display webworker traces also? just an idea

Possibly this is a 'samtools calmd' analog in CRAM form too. We will follow up in email with sacha

Ref here https://sourceforge.net/p/samtools/mailman/message/36681818/ Apparently samtools can resolve SNPs between this and a refseq from what I can tell, creating both a MD and CIGAR string from samtools view file.cram

nice work! it may be worth adding some testing to make sure this matches samtools decoding. we have our own "read features to cigar string" in jbrowse that uses code...

in the absense of 'synthesizing' read features from thin air, one way to test is to use samtools on a small test file (we have some test files in test/data/...