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Ignore undeclared keys in INFO and FORMAT when writing BCF files #169

Merged
merged 2 commits into from
Jul 1, 2019
Merged

Ignore undeclared keys in INFO and FORMAT when writing BCF files #169

merged 2 commits into from
Jul 1, 2019

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alumi
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@alumi alumi commented Jul 1, 2019

cljam.io.bcf.writer/write-variants fails to encode variants if they contain keys not declared in meta-info.
This PR fixes the bug by ignoring such keys.

cljam/test/cljam/io/bcf/writer_test.clj

Lines 256 to 258 in 94ce1f8

[{:chr "1", :pos 10, :ref "A", :alt ["C"],
:info {:UNDECLARED-INFO #{"???"}},
:FORMAT [:UNDECLARED-FORMAT]}]

https://travis-ci.org/chrovis/cljam/jobs/552587080#L535-L554

@alumi alumi added the bug label Jul 1, 2019
@alumi alumi requested a review from a team July 1, 2019 05:10
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codecov bot commented Jul 1, 2019 •
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Codecov Report

Merging #169 into master will not change coverage.
The diff coverage is 100%.

Impacted file tree graph

@@           Coverage Diff           @@
##           master     #169   +/-   ##
=======================================
  Coverage   86.87%   86.87%           
=======================================
  Files          73       73           
  Lines        5663     5663           
  Branches      481      481           
=======================================
  Hits         4920     4920           
  Misses        262      262           
  Partials      481      481
Impacted Files Coverage Δ
src/cljam/io/bcf/writer.clj 89.85% <100%> (ø) ⬆️

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@alumi alumi requested review from a team and removed request for a team July 1, 2019 05:21
@ghost ghost requested review from athos and yito88 and removed request for a team July 1, 2019 05:21
yito88
yito88 approved these changes Jul 1, 2019
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LGTM!

@alumi alumi mentioned this pull request Jul 1, 2019
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athos
athos approved these changes Jul 1, 2019
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LGTM 👍

@athos athos merged commit 2cbb76f into master Jul 1, 2019
@athos athos deleted the fix/bcf-ignore-undeclared-keys branch July 1, 2019 10:28
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@yito88 yito88 yito88 approved these changes

@athos athos athos approved these changes

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@alumi @athos @yito88