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Add more gVCF support #991
This PR attempts to add more support for GVCF, breaking from #847 to allow that PR to be more single topic
Most gVCF files consists of blocks of "<NON_REF>" calls that span a range (e.g. it uses the END= info field).
Some special cases
Several sample data test files are added, including gatk haplotype caller run in gvcf mode run over the volvox-sorted bam file :)
This looks good, except for the HTML-entitizing of all detail fields. I think that needs to be somehow limited to VCF details
I reverted the html-entitizing and the display didn't look any different to me, but maybe I'm looking at the wrong thing.
anyway, a little-known feature of the detailmixin is: if a thing (any data type) has a toHTML method on it, the detail page will call it and display that HTML. So, you could add toHTML methods to some things in VariantDetailMixin, maybe?
The <*> actually doesn't cause problems but other symbolic alleles do including DEL:ME in the volvox test data and <NON_REF> from gvcf and other things. Note that on the current live jbrowse.org instance, it just displays 1|1 in the genotype field on the DEL:ME in the genotype table, but with this PR it tries to pull the actual alt allele text (as it should IMO) into the genotype table
Here's a screenshot displaying the issue
The encoding entities nicely fixed both the the alternative allele field and the genotype table but possibly could look for another workaround