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macieksmuga srblum adamnovak glennhickey

hgvm's Issues

Decoupling classic and graph mode in server by introducing new GraphBackend class

Make slides for HGVM for lab meeting 2015-05-13

Get more comment on ga4gh pull request on alleles (https://github.com/ga4gh/schemas/pull/281)

Make hal2sg import Cactus SNPs correctly

Convert cactus hal alignments for each test region to Maciek format

Write reference server joins/search endpoint

Make halStats report coverage of each genome against anything else, all at once

assemble second "jump" PR in server to update to latest schemas

Make pull request on sequence annotation subgraphs

Make allele graph figures to explain David's graph comparison for the bake-off

Fix hal2sg to output in SQL schema compliant format

Pass off data to Adam: CENX hg38, CENX 2kb consensus, and CENX associated quality trimmed reads

Write sequences/{id}/bases endpoint for reference server

Make Adam's ARCS Symposium HGVM Poster

Send poster cactus/camel evaluation plots to Benedict

Make easy revisions to the string mapping paper

Organise presentation for next reference variation call on 29th of April

Demoing Cactus and Camel.

Write point-by-point review response

Replace Cactus vs. Camel graphs using working hal2sg, before sending progress report in

Create presentation describing competition phase of HGVM / include description of Karen's region

Put CENX regions in Maciek's format

Send someone to pitch graphs at Google

Bring hal2sg into compliance with final SQL format

Get Cactus alignments into sql-lite format

Add documentation to graph branch of server

carve out and submit issue PR's to schemas repo

Rewrite sequences/search endpoint for reference server

Make hal2sg not put joins on the wrong ends of bases

Refactor hal2sg to equate "forward" with the left side of SGSide

SGSide class uses forward flag in opposite sense (forward=right) as AVRO spec (forward=left). Bandaid solution in place to flip when writing SQL output, but code should be refactored to use correct definition throughout.

write allele paths endpoint for reference server

Cleanup the wiki for the HGVM bakeoff

Rewrite references/search endpoint for reference server

Send Karen the SQL format, help with conversion

Import VG into SideGraph

Fix up 281 with single inheritance, Alleles in VariantSets

Make progress report draft

Put up Karen's centromere data with the other pilot regions

Tidy up / document graph sql-lite schema format

Compare Cactus to Camel

Fix subgraph searches in graph server

Improve Cactus output vis a vis Adams evaluation

Cactus (default parameters, star tree) alignments not looking so great in current evaluation. Notably, there seem to be too many paralogs. Need to tweak parameters (possibly using Joel's new method) to improve this.

Run VG on our pilot regions and enter it in the contest

Make presentations on evaluations for May 13, with an eye to figures for the progress report draft due 4/8

Evaluate Camel against itself to tune parameters