vgteam/sequencetubemap issues and pull requests

#98 - track.indexSequence contains many NaN elements

Issue - State: closed - Opened by a2htray almost 4 years ago - 1 comment

#97 - Error loading sequenceTubeMap

Issue - State: closed - Opened by brettChapman about 4 years ago - 10 comments

#96 - Bump http-proxy from 1.17.0 to 1.18.1

Pull Request - State: closed - Opened by dependabot[bot] about 4 years ago - 1 comment
Labels: dependencies

#95 - Bump handlebars from 4.1.2 to 4.7.6

Pull Request - State: closed - Opened by dependabot[bot] about 4 years ago - 1 comment
Labels: dependencies

#94 - fix for #93

Pull Request - State: closed - Opened by Nheyer about 4 years ago - 1 comment

#93 - generateTrackIndexSequences returns negative values when there are no negative array members

Issue - State: closed - Opened by Nheyer about 4 years ago - 6 comments

#92 - Bump elliptic from 6.4.1 to 6.5.3

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#91 - Question on the legend

Issue - State: open - Opened by Nheyer over 4 years ago - 2 comments

#90 - Failed to display the alt path in sequenceTubeMap server

Issue - State: open - Opened by songtaogui over 4 years ago

#89 - Bump websocket-extensions from 0.1.3 to 0.1.4

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#88 - confusion with genomic positions (coordinate axis) of minus strand genes

Issue - State: closed - Opened by LilithElina over 4 years ago - 4 comments

#87 - Bump acorn from 5.7.3 to 5.7.4

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#86 - Bump handlebars from 4.1.2 to 4.5.3

Pull Request - State: closed - Opened by dependabot[bot] almost 5 years ago - 1 comment
Labels: dependencies

#85 - How to add options to URL

Issue - State: closed - Opened by songtaogui almost 5 years ago - 2 comments

#84 - Bump eslint-utils from 1.3.1 to 1.4.3

Pull Request - State: closed - Opened by dependabot[bot] about 5 years ago - 1 comment
Labels: dependencies

#83 - Bump mixin-deep from 1.3.1 to 1.3.2

Pull Request - State: closed - Opened by dependabot[bot] about 5 years ago - 1 comment
Labels: dependencies

#82 - Bump lodash.template from 4.4.0 to 4.5.0

Pull Request - State: closed - Opened by dependabot[bot] about 5 years ago - 1 comment
Labels: dependencies

#81 - Drop paths starting with "_" from the positional path list

Pull Request - State: closed - Opened by adamnovak about 5 years ago

#80 - Receiving "warning:[XG] Loading an out-of-date XG format" with newest version of vg

Issue - State: open - Opened by briannadon about 5 years ago - 3 comments

#79 - Deselecting "Show sequence reads" breaks IVG completely

Pull Request - State: closed - Opened by subwaystation over 5 years ago

#78 - Deselecting "Show sequence reads" breaks IVG completely

Issue - State: closed - Opened by subwaystation over 5 years ago - 1 comment

#77 - Report vg chunk errors more verbosely

Pull Request - State: closed - Opened by adamnovak over 5 years ago

#76 - Docker with sequenceTubeMap server and VG?

Issue - State: open - Opened by keiranmraine over 5 years ago - 2 comments

#75 - Screen goes blank if you select a region starting at a node ID that does not have any threads associated with it

Issue - State: open - Opened by jeizenga over 5 years ago - 7 comments

#74 - Visualization sometimes changes dramatically between starting the region from two adjacent nodes

Issue - State: open - Opened by jeizenga over 5 years ago - 1 comment

#73 - Choosing "Nodes" as the unit seems to still select a region in units of sequence length

Issue - State: open - Opened by jeizenga over 5 years ago - 1 comment

#72 - Transparent nodes

Pull Request - State: closed - Opened by wolfib almost 6 years ago

#71 - Softclip on the left of a reverse-strand read is displayed reversed

Issue - State: open - Opened by adamnovak almost 6 years ago

#70 - Make server port a constant so it can be changed

Pull Request - State: closed - Opened by adamnovak almost 6 years ago

#69 - Can't drag to pan vertically anymore

Issue - State: open - Opened by adamnovak almost 6 years ago
Labels: good-first-issue

#68 - Crazy graph layout causes crash when GAM is given

Issue - State: closed - Opened by eldariont about 6 years ago - 4 comments

#67 - Disabling a haplotype path causes graph to disappear

Issue - State: closed - Opened by eldariont about 6 years ago - 5 comments

#66 - Build of docker container fails

Issue - State: closed - Opened by eldariont about 6 years ago - 5 comments

#65 - Display error with lots of warnings on the browser console

Issue - State: closed - Opened by eldariont about 6 years ago - 5 comments

#64 - Mouse-over node IDs are confusing with redundant nodes removed

Issue - State: open - Opened by jeizenga about 6 years ago
Labels: good-first-issue

#63 - TubeMap requires both RocksDB and .gai index

Issue - State: closed - Opened by jeizenga about 6 years ago - 3 comments

#62 - Make data preprocessing scripts match current vg indexing API

Issue - State: closed - Opened by jeizenga about 6 years ago - 2 comments

#61 - It is not possible to supply custom data to the tube map

Issue - State: closed - Opened by ekg about 6 years ago - 2 comments

#60 - prepare scripts aren't executable

Issue - State: closed - Opened by glennhickey over 6 years ago - 1 comment

#59 - Zooming Functionalities

Pull Request - State: closed - Opened by jachansantiago over 6 years ago

#58 - Move buffering to fix #56

Pull Request - State: closed - Opened by adamnovak over 6 years ago

#57 - mountedData is not created when following the README instructions

Issue - State: closed - Opened by adamnovak over 6 years ago - 1 comment

#56 - Cannot build frontend

Issue - State: closed - Opened by cartoonist over 6 years ago - 4 comments

#55 - Updated frontend

Pull Request - State: closed - Opened by tanessav over 6 years ago

#54 - Updated frontend pages

Pull Request - State: closed - Opened by tanessav over 6 years ago

#53 - Update checkbox states across page refreshes #34

Pull Request - State: closed - Opened by tanessav over 6 years ago - 1 comment

#52 - Error improvements

Pull Request - State: closed - Opened by adamnovak over 6 years ago

#51 - Handle out of bound user inputs #39

Pull Request - State: closed - Opened by tanessav over 6 years ago

#50 - Add Reload Data Files Buttons

Pull Request - State: closed - Opened by tanessav over 6 years ago - 1 comment

#49 - Merge paragraph / vg changes

Pull Request - State: closed - Opened by pkrusche over 6 years ago

#48 - Pull in changes from Illumina fork

Issue - State: open - Opened by adamnovak over 6 years ago

#47 - Reload Data Files Button

Issue - State: closed - Opened by adamnovak over 6 years ago

#46 - Align read from text box and display it

Issue - State: open - Opened by adamnovak over 6 years ago

#45 - View GAM JSON from browser on tube map

Issue - State: open - Opened by adamnovak over 6 years ago

#44 - Display read mapping quality in alpha or shade channel

Issue - State: closed - Opened by adamnovak over 6 years ago - 1 comment

#43 - Substitutions can render out of bounds of nodes when alignments aren't really to the right graph

Issue - State: open - Opened by adamnovak over 6 years ago - 1 comment

#42 - wrong repo lol

Issue - State: closed - Opened by wheaton5 almost 7 years ago

#41 - Put temporary files in directories

Pull Request - State: closed - Opened by adamnovak almost 7 years ago

#40 - Reference paths sometimes extend one node further than haplotypes

Issue - State: open - Opened by adamnovak almost 7 years ago - 1 comment

#39 - Out of bounds node ID crashes vg on the backend

Issue - State: closed - Opened by adamnovak almost 7 years ago

#38 - Ability to pull in haplotypes relevant to a context around a node

Issue - State: open - Opened by adamnovak almost 7 years ago

#37 - US: Link to current view

Issue - State: closed - Opened by adamnovak almost 7 years ago
Labels: good-first-issue, qol

#36 - US: Copy Node Sequence

Issue - State: open - Opened by adamnovak almost 7 years ago - 2 comments
Labels: good-first-issue, qol

#35 - Reads going out of bounds on the left aren't visible, while on the right they are cut off

Issue - State: open - Opened by adamnovak almost 7 years ago - 4 comments
Labels: good-first-issue

#34 - Checkbox states are retained across page refreshes by the browser and the frontend doesn't notice

Issue - State: closed - Opened by adamnovak almost 7 years ago

#33 - Add gbwt

Pull Request - State: closed - Opened by adamnovak almost 7 years ago - 2 comments

#32 - Cross-talk between simultaneous queries

Issue - State: closed - Opened by adamnovak almost 7 years ago

#31 - Adopt a 2-layer way to do the configs

Pull Request - State: closed - Opened by adamnovak almost 7 years ago

#30 - GBWT as Haplotype Source

Issue - State: closed - Opened by adamnovak almost 7 years ago

#29 - command line version

Issue - State: closed - Opened by ekg almost 7 years ago - 1 comment

#28 - Add lessons learned from my manual installation to the README

Pull Request - State: closed - Opened by adamnovak almost 7 years ago

#27 - Can I arrange all the nodes on the selected path horizontally as possible?

Issue - State: open - Opened by 6br almost 7 years ago

#26 - Path is not in sorted order by rank

Issue - State: closed - Opened by ifiddes-10x-zz almost 7 years ago - 2 comments

#25 - D3.js Version

Issue - State: closed - Opened by subwaystation almost 7 years ago - 4 comments

#24 - Fix: currentNodeIsForward

Pull Request - State: closed - Opened by 6br almost 7 years ago - 1 comment

#23 - Handling of paths that leave and re-enter the displayed subgraph

Issue - State: open - Opened by 6br almost 7 years ago - 3 comments
Labels: good-first-issue

#22 - vg chunk problem with newer vg docker image v1.5.0-2018-g71f96239-t119-run

Issue - State: closed - Opened by Imoteph almost 7 years ago - 2 comments

#21 - Scaling Issue of Drawn Bases when Zooming.

Issue - State: open - Opened by subwaystation about 7 years ago - 5 comments
Labels: good-first-issue

#20 - Raise an error on selecting the path shown in the bottom

Issue - State: open - Opened by 6br about 7 years ago - 4 comments

#19 - Obtain visualization on the command line

Issue - State: open - Opened by ekg about 7 years ago - 3 comments

#18 - Work on Docker/custom file support

Issue - State: closed - Opened by adamnovak about 7 years ago

#17 - Make minor improvements to the tube map

Issue - State: closed - Opened by adamnovak about 7 years ago

#16 - Distinguish softclips

Issue - State: closed - Opened by adamnovak about 7 years ago

#15 - Add substitutions to display

Issue - State: closed - Opened by adamnovak about 7 years ago

#14 - Revise insertion display

Issue - State: closed - Opened by adamnovak over 7 years ago - 1 comment

#13 - US: Multi-sample read pileups

Issue - State: open - Opened by cmarkello over 7 years ago

#12 - US: Element selection

Issue - State: open - Opened by adamnovak over 7 years ago

#11 - US: Node ID search

Issue - State: closed - Opened by adamnovak over 7 years ago - 1 comment

#10 - US: GRCh38 coordinate search

Issue - State: closed - Opened by adamnovak over 7 years ago - 6 comments

#9 - US: More zoom

Issue - State: closed - Opened by adamnovak over 7 years ago

#8 - US: Common difference identification

Issue - State: closed - Opened by adamnovak over 7 years ago - 4 comments

#7 - US: Read/reference difference display

Issue - State: closed - Opened by adamnovak over 7 years ago - 1 comment

#6 - US: .xg thread and path display

Issue - State: closed - Opened by adamnovak over 7 years ago - 1 comment

#5 - US: Custom read set display

Issue - State: closed - Opened by adamnovak over 7 years ago - 1 comment

#4 - US: .gam/.vg upload

Issue - State: closed - Opened by adamnovak over 7 years ago - 3 comments

#3 - US: .vg drag and drop

Issue - State: open - Opened by adamnovak over 7 years ago

#2 - US: Display reads, reference, and haplotypes

Issue - State: closed - Opened by adamnovak over 7 years ago - 2 comments

#1 - README is out of date

Issue - State: open - Opened by jdidion over 7 years ago - 1 comment

GitHub / vgteam/sequencetubemap issues and pull requests