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Fix parsing SAM header values containing ':'. #123

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merged 1 commit into from
Dec 7, 2017
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@alumi alumi commented Dec 6, 2017

Summary

Don't discard substring after second : when parsing SAM header.

Problem

Complex SAM headers can be modified unexpectedly.

input sam
@SQ	SN:A:B;100-200;++;chr1:100-200	LN:400
output sam
@SQ	SN:A	LN:400

Cause

(clojure.string/split "SN:A:B;100-200;++;chr1:100-200" #":")
; => ["SN" "A" "B;100-200;++;chr1" "100-200"]

clojure.string/split with 2 args splits given string at all ocurrence of the regex.

Changes

Pass 2 as 3rd arg (limit) of clojure.string/split.

Affects

SAM/BAM I/O

Tests

  • lein test :all 🆗

@alumi alumi added the bug label Dec 6, 2017
@alumi alumi requested a review from totakke December 6, 2017 10:00
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codecov bot commented Dec 6, 2017

Codecov Report

Merging #123 into master will not change coverage.
The diff coverage is 100%.

Impacted file tree graph

@@           Coverage Diff           @@
##           master     #123   +/-   ##
=======================================
  Coverage   84.81%   84.81%           
=======================================
  Files          62       62           
  Lines        4196     4196           
  Branches      415      415           
=======================================
  Hits         3559     3559           
  Misses        222      222           
  Partials      415      415
Impacted Files Coverage Δ
src/cljam/io/sam/util.clj 89.58% <100%> (ø) ⬆️

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@totakke totakke merged commit 649204b into master Dec 7, 2017
@totakke totakke deleted the fix/sam-header branch December 7, 2017 08:03
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totakke commented Dec 7, 2017

Thank you 😄

@alumi
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alumi commented Dec 7, 2017

Thank you for reviewing! 😸

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2 participants