feat: add bed file datafetcher #877

etowahadams · 2023-04-19T03:45:38Z

Fix #583
Toward #870

Change List

Add support for BED files
Refactor CSV data fetcher

Test out using this gist: http://localhost:3000/?gist=etowahadams/cd49a7f308e4859e095d209056a564d3

Documentation PR

Checklist

Ensure the PR works with all demos on the online editor
Unit tests added or updated
Examples added or updated
Documentation updated (e.g., added API functions)
Screenshots for visual changes (e.g., new encoding support or UI change on Editor)

…ang/gosling.js into etowahadams/make-bed-primitive

tsconfig.json

etowahadams · 2023-05-02T15:58:00Z

package.json

@@ -155,7 +157,7 @@
 },
 "husky": {
 "hooks": {
- "pre-commit": "run-p changelog schema schema-higlass schema-theme schema-template format && git add .",


Sometimes I only want to commit things that are staged. When the pre-commit hook would run, it would add all my unstaged files

I see. Would the generated schema files and the changelogs still be included by the pre-commit hooks?

Ah you're right. I'll add it back.

@manzt Do you aware of any better way to deal with this?

I think this is something we could probably check in CI? For example, we could have a GitHub action that runs a package.json script and assert that there are no git changes. If there are, fail and require the developer to run locally in order to pass CI. This way we allow much more flexibility when creating PRs, but ensure the changelog and schemas must be in sync in order to be merged into master.

I personally really dislike pre-commit hooks because I commit often.

I like the idea! I also dislike waiting for the pre-commit hooks to run scripts.

src/data-fetchers/bed/bed-parser.ts

sehilyi

This is awesome! I left several minor comments.

Also, do you want to add a simple example to our example gallery? That would be really great to include.

sehilyi · 2023-05-03T15:57:54Z

package.json

@@ -155,7 +157,7 @@
 },
 "husky": {
 "hooks": {
- "pre-commit": "run-p changelog schema schema-higlass schema-theme schema-template format && git add .",


I see. Would the generated schema files and the changelogs still be included by the pre-commit hooks?

src/core/init.ts

src/data-fetchers/bed/bed-worker.ts

src/data-fetchers/bed/bed-parser.ts

src/data-fetchers/bed/bed-parser.test.ts

src/data-fetchers/bed/bed-parser.ts

src/data-fetchers/bed/shared-types.ts

Co-authored-by: Sehi L'Yi <[email protected]>

…ang/gosling.js into etowahadams/make-bed-primitive merge remote commits

etowahadams · 2023-05-06T04:23:54Z

Finished making edits, just need to add the example.

etowahadams · 2023-05-06T18:51:37Z

Added example, ready to merge

etowahadams added 27 commits April 18, 2023 23:42

feat: add bed file datafetcher

e1cdd35

fix: add types and refactor csv-data-fetcher

872acf2

fix: pull out some constructor logic into function

4d369a9

docs: comments to schema

92aef50

fix: make function to calculate cumulative position

f0b19cc

fix: remove unused import

51282c6

feat(bed-data-fetcher): parsing functions

0259738

refactor(bed-data-fetcher): make tiles function async

a90b3f9

refactor(bed-data-fetcher): add types, refine tests

2d2c932

refactor(csv-data-fetcher): finish adding types

04682a3

test(bed-data-fetcher): add more tests for custom columns

052d4bc

feat(bed-data-fetcher): add tabix bed data fetcher

4c9be09

feat(bed-data-fetcher): add support for custom column names

e18300d

refactor(bed-data-fetcher): move around functions for clarity

2ca3a2c

refactor(bed-worker): make bed parser create a line parser

d0c3a64

fix(bed-data-fetcher): change fetcher name

25047d4

fix: remove git add from pre-commit hook

8c8bc50

refactor: move emptyTile to utils

23873a3

fix: missing semicolon

4658e0e

fix: update bbi

869d45e

test(csv-data-fetcher): add types to tests

917a702

refactor(bed-data-fetcher): separate shared types

166e2fe

test: write bed parser tests

99671da

Merge branch 'master' into etowahadams/make-bed-primitive

ce7740b

fix: update schema

2219728

Merge branch 'etowahadams/make-bed-primitive' of github.com:gosling-l…

90fd850

…ang/gosling.js into etowahadams/make-bed-primitive

fix: typo

d5103dc

etowahadams commented Apr 29, 2023

View reviewed changes

tsconfig.json Outdated Show resolved Hide resolved

etowahadams added 2 commits April 28, 2023 22:18

fix: remove console-warns, rename parser

cd636ea

docs: improve schema description

69989f3

fix: typo

cefb9dd

etowahadams mentioned this pull request Apr 29, 2023

docs: add bed file documentation gosling-lang/gosling-website#63

Merged

etowahadams marked this pull request as ready for review April 29, 2023 04:19

etowahadams requested a review from sehilyi April 29, 2023 04:19

etowahadams added 3 commits May 2, 2023 11:00

refactor: make bed parser resemble vcf parser

6e5071f

fix: add d3 types

de0f338

refactor: add types to CSV data fetcher

c8347dd

etowahadams commented May 2, 2023

View reviewed changes

src/data-fetchers/bed/bed-parser.ts Show resolved Hide resolved

sehilyi approved these changes May 3, 2023

View reviewed changes

etowahadams and others added 9 commits May 5, 2023 16:55

refactor: based on code review

65dee0b

fix: change type import

1343bd5

refactor: make if logic clearer in bed-parser.ts

ca8dcfd

Co-authored-by: Sehi L'Yi <[email protected]>

docs: add comments to custom header logic

023bf8a

fix: remove unused param

c6b33b4

Co-authored-by: Sehi L'Yi <[email protected]>

refactor: make parser params more explicit

457767e

Merge branch 'etowahadams/make-bed-primitive' of github.com:gosling-l…

ab0da23

…ang/gosling.js into etowahadams/make-bed-primitive merge remote commits

fix: bed-parser tests

ffc072f

fix: add bed to typecheck

2979329

manzt mentioned this pull request May 6, 2023

ci: move pre-commit checks to CI #893

Merged

5 tasks

etowahadams added 3 commits May 6, 2023 13:49

feat: add BED example

118812a

Merge branch 'master' into etowahadams/make-bed-primitive

ce5b690

fix: missing space

4967870

etowahadams merged commit a087340 into master May 6, 2023

etowahadams deleted the etowahadams/make-bed-primitive branch May 6, 2023 19:03

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feat: add bed file datafetcher #877

feat: add bed file datafetcher #877

etowahadams commented Apr 19, 2023 •

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etowahadams commented May 6, 2023

feat: add bed file datafetcher #877

feat: add bed file datafetcher #877

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etowahadams commented Apr 19, 2023 • edited Loading

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