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Allow ability to enter a space-separated locstring to open a list of regions #2741

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merged 9 commits into from
Mar 9, 2022

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@cmdcolin cmdcolin commented Feb 14, 2022

This allows the ability to enter a locstring like "ctgA:1..100 ctgB:1..100" and it will open those two regions up side by side

Screenshot from 2022-02-14 14-11-11

Fixes #272

@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Feb 14, 2022
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codecov bot commented Feb 14, 2022

Codecov Report

Merging #2741 (5bc6d83) into main (06db2c4) will decrease coverage by 0.01%.
The diff coverage is 82.60%.

Impacted file tree graph

@@            Coverage Diff             @@
##             main    #2741      +/-   ##
==========================================
- Coverage   60.16%   60.14%   -0.02%     
==========================================
  Files         577      577              
  Lines       26675    26642      -33     
  Branches     6494     6471      -23     
==========================================
- Hits        16049    16024      -25     
+ Misses      10299    10293       -6     
+ Partials      327      325       -2     
Impacted Files Coverage Δ
.../linear-genome-view/src/LinearGenomeView/index.tsx 85.27% <82.35%> (+1.29%) ⬆️
packages/core/util/index.ts 85.64% <83.33%> (+0.25%) ⬆️
...s/svg/src/SvgFeatureRenderer/components/Chevron.js 87.17% <0.00%> (-10.26%) ⬇️
...gins/svg/src/SvgFeatureRenderer/components/util.ts 92.72% <0.00%> (-1.82%) ⬇️
...gFeatureRenderer/components/ProcessedTranscript.js 85.13% <0.00%> (-1.36%) ⬇️
packages/core/util/layouts/GranularRectLayout.ts 86.75% <0.00%> (-0.43%) ⬇️
packages/core/util/analytics.ts 91.83% <0.00%> (+2.04%) ⬆️

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@cmdcolin cmdcolin added enhancement New feature or request and removed needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) labels Feb 14, 2022
@cmdcolin cmdcolin requested a review from rbuels February 15, 2022 00:34
@cmdcolin cmdcolin marked this pull request as draft February 16, 2022 18:23
@cmdcolin cmdcolin force-pushed the space_separated_locstring branch 3 times, most recently from f19ae41 to 1f6e72d Compare February 23, 2022 02:09
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This now let's you enter a list of strings such as "ctgA ctgB" and it will load those two chromosomes. this was mentioned as a weakness of the current state of this branch when it was discussed at a meeting (previously required fully-qualified locstrings like ctgA:1-100, not just ctgA)

You can also specify a list of space separated regions such as "ctgA:1-100 ctgB:1-100"

it also let's you do some stuff like "{hg19}1:1..100 {hg38}1:1..100" to load multiple assemblies side by side,kind of obscure but...fun

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note that the multiple assembly side by side will pretty quickly hit errors like this in most cases

Screenshot from 2022-02-22 19-15-18

@cmdcolin cmdcolin marked this pull request as ready for review March 1, 2022 22:23
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cmdcolin commented Mar 3, 2022

this PR now allows creating reversed regions by adding [rev] after your coordinates

example 1: I enter chr1:1-100[rev] this will navigate to chr1:100 in the reversed orientation (does not create a displayed region of chr1:1-100, assumed that displayed region should be entirety of chr1)
example 2: I enter "chr1:1-100[rev] chr2:1-100" this creates two displayed regions "chr1:1-100, in the reverse orientation, and chr2:1-100, forward orientation" (assumed that the displayed regions are fragments of the inputted regions,

@cmdcolin cmdcolin merged commit c7b8ff0 into main Mar 9, 2022
@cmdcolin cmdcolin deleted the space_separated_locstring branch March 9, 2022 18:36
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generate displayed regions from space-separated locstring
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