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Make softclip indicator black if no seq available #1574

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merged 3 commits into from
Dec 21, 2020

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cmdcolin
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This makes it so that the softclip indicator is colored black if no sequence is available to draw

Also adds a FAQ entry about this

Addresses #1562

localhost_3000__config=test_data%2Fconfig_demo json session=local-oYPHZEK9O

@cmdcolin cmdcolin force-pushed the softclip_indicator_black_if_no_seq branch from b7a232a to 7a8cc52 Compare December 20, 2020 00:46
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codecov bot commented Dec 20, 2020

Codecov Report

Merging #1574 (3e25c7d) into master (f033ae9) will decrease coverage by 0.01%.
The diff coverage is 77.77%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #1574      +/-   ##
==========================================
- Coverage   59.51%   59.50%   -0.02%     
==========================================
  Files         435      435              
  Lines       19565    19568       +3     
  Branches     4568     4569       +1     
==========================================
- Hits        11645    11644       -1     
- Misses       7626     7630       +4     
  Partials      294      294              
Impacted Files Coverage Δ
...ns/alignments/src/PileupRenderer/PileupRenderer.ts 90.72% <77.77%> (-1.17%) ⬇️
...inearGenomeView/components/RefNameAutocomplete.tsx 86.20% <0.00%> (-3.45%) ⬇️

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@cmdcolin cmdcolin force-pushed the softclip_indicator_black_if_no_seq branch from 7a8cc52 to c462f86 Compare December 20, 2020 20:01
plugins/alignments/src/PileupRenderer/PileupRenderer.ts Outdated Show resolved Hide resolved
Comment on lines -373 to +378
// Black accounts for IUPAC ambiguity code bases such as N that show in soft clipping
ctx.fillStyle = lighten(colorForBase[base] || '#000000', 0.3)
// Black accounts for IUPAC ambiguity code bases such as N that
// show in soft clipping
const baseColor = colorForBase[base] || '#000000'
ctx.fillStyle = baseColor
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It looks like the lightening of the color of the softclipped bases was removed. We can use theme.palette.bases.<base>.light to keep that behavior.

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Forgot to mention but I propose removing the lightening. We now render the clip indicator in all cases, even when soft clip is showing, so that it is clear when bases are being drawn beyond that)

@cmdcolin cmdcolin merged commit b9f3515 into master Dec 21, 2020
@cmdcolin cmdcolin added the enhancement New feature or request label Dec 21, 2020
@cmdcolin cmdcolin deleted the softclip_indicator_black_if_no_seq branch December 22, 2020 02:24
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2 participants