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Fix breakpoint split view showing too many connections for paired end ends #1534

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merged 2 commits into from
Dec 9, 2020

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@cmdcolin cmdcolin commented Dec 9, 2020

The breakpoint split view when plotting the paired read connections across chromosomes uses the fact that the flag is NOT "read mapped in proper pair" https://broadinstitute.github.io/picard/explain-flags.html?flag=100

But it was using the old flag helpers which were removed. Instead we check bitwise ops on the flag

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codecov bot commented Dec 9, 2020

Codecov Report

Merging #1534 (2032c4c) into master (20b12f3) will decrease coverage by 0.00%.
The diff coverage is 30.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #1534      +/-   ##
==========================================
- Coverage   59.49%   59.48%   -0.01%     
==========================================
  Files         435      435              
  Lines       19535    19538       +3     
  Branches     4555     4552       -3     
==========================================
  Hits        11622    11622              
- Misses       7618     7621       +3     
  Partials      295      295              
Impacted Files Coverage Δ
plugins/breakpoint-split-view/src/model.ts 43.51% <30.00%> (+0.54%) ⬆️
packages/core/util/analytics.ts 75.60% <0.00%> (-2.44%) ⬇️
...ins/wiggle/src/LinearWiggleDisplay/models/model.ts 81.98% <0.00%> (-0.91%) ⬇️

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@cmdcolin cmdcolin changed the title Make the breakpoint split view use the flags variable instead of flag helpers Fix breakpoint split view showing too many connections for paired end ends Dec 9, 2020
@cmdcolin cmdcolin marked this pull request as ready for review December 9, 2020 16:40
@cmdcolin cmdcolin merged commit 2fb836d into master Dec 9, 2020
@cmdcolin cmdcolin deleted the fix_paired_read_breakpoint_split_view branch December 9, 2020 18:35
@cmdcolin cmdcolin added the bug Something isn't working label Dec 21, 2020
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