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Fix parsing comma-separated number in region #111

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merged 1 commit into from Sep 19, 2017

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totakke
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@totakke totakke commented Sep 19, 2017

Adds support of comma-separated number in region.

(region/parse-region "chr1:1,000-2,000")
;;=> {:chr "chr1", :start 1000, :end 2000}

SAMtools also supports such numbers.

5. A region should be presented in one of the following formats:
   `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is
   specified, the input alignment file must be a sorted and indexed
   alignment (BAM/CRAM) file.

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codecov bot commented Sep 19, 2017

Codecov Report

Merging #111 into master will not change coverage.
The diff coverage is 100%.

Impacted file tree graph

@@          Coverage Diff           @@
##           master    #111   +/-   ##
======================================
  Coverage    85.5%   85.5%           
======================================
  Files          62      62           
  Lines        4085    4085           
  Branches      399     399           
======================================
  Hits         3493    3493           
  Misses        193     193           
  Partials      399     399
Impacted Files Coverage Δ
src/cljam/util/region.clj 100% <100%> (ø) ⬆️

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@alumi alumi merged commit e32b8b2 into master Sep 19, 2017
@alumi alumi deleted the fix/parse-region-with-comma branch September 19, 2017 06:34
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alumi commented Sep 19, 2017

Merged. Thank you for the fix 👍

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2 participants