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Add support cloning VCF/BCF. #200

Merged
merged 2 commits into from
Jun 5, 2020
Merged

Add support cloning VCF/BCF. #200

merged 2 commits into from
Jun 5, 2020
+47 −6

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niyarin
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@niyarin niyarin commented Jun 3, 2020

This PR adds a function to create a new object by copying except stream when VCF/BCF object is put in the reader.
This function is almost the same as "cljam.io.bam.core/clone-reader".

@niyarin niyarin requested review from alumi and a team as code owners June 3, 2020 09:25
@niyarin niyarin requested review from athos and removed request for a team June 3, 2020 09:25
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codecov bot commented Jun 3, 2020 •
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Codecov Report

Merging #200 into master will increase coverage by 0.01%.
The diff coverage is 88.46%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #200      +/-   ##
==========================================
+ Coverage   86.90%   86.91%   +0.01%     
==========================================
  Files          77       77              
  Lines        6246     6267      +21     
  Branches      519      520       +1     
==========================================
+ Hits         5428     5447      +19     
- Misses        299      300       +1     
- Partials      519      520       +1
Impacted Files Coverage Δ
src/cljam/io/vcf.clj 94.36% <88.46%> (-1.64%) ⬇️

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alumi
alumi reviewed Jun 5, 2020
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Thanks! 👍 Looks good except a reflection warning

src/cljam/io/vcf.clj Outdated
(BCFReader. (.url rdr) (.meta-info rdr) (.header rdr)
input-stream (.start-pos rdr) (.index-delay rdr))))

(defn clone-reader
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Suggested change
(defn clone-reader
(defn ^Closeable clone-reader

alumi
alumi approved these changes Jun 5, 2020
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👍 👍

athos
athos approved these changes Jun 5, 2020
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LGTM 👍 Thanks for your contribution!

@athos athos merged commit 84a535d into master Jun 5, 2020
@athos athos deleted the feature/clone-vcf branch June 5, 2020 05:39
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niyarin commented Jun 5, 2020

Thanks for the review!

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@alumi alumi alumi approved these changes

@athos athos athos approved these changes

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3 participants
@niyarin @athos @alumi