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Fix parser of optional fields in SAM/BAM. #92

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merged 1 commit into from
Jul 31, 2017
Merged

Fix parser of optional fields in SAM/BAM. #92

merged 1 commit into from
Jul 31, 2017

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alumi
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@alumi alumi commented Jul 31, 2017

Fixed returned type of following two elements in optional fields in SAM/BAM.

type description module type (before) type (after)
A Printable character bam byte char
H Byte array in the Hex format sam nil byte-array

@alumi alumi added the bug label Jul 31, 2017
@alumi alumi requested a review from totakke July 31, 2017 05:39
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codecov bot commented Jul 31, 2017 •
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Codecov Report

Merging #92 into master will increase coverage by 0.29%.
The diff coverage is 75%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #92      +/-   ##
==========================================
+ Coverage   82.93%   83.22%   +0.29%     
==========================================
  Files          60       60              
  Lines        4161     4162       +1     
  Branches      452      452              
==========================================
+ Hits         3451     3464      +13     
+ Misses        258      246      -12     
  Partials      452      452
Impacted Files Coverage Δ
src/cljam/io/sam/util.clj 89.62% <100%> (+2.54%) ⬆️
src/cljam/io/bam/decoder.clj 70.21% <66.66%> (+4.25%) ⬆️

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totakke
totakke reviewed Jul 31, 2017
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Thanks for the fix. I have a question about reinvention. Please check it.

src/cljam/io/sam/util.clj Outdated
@@ -77,6 +77,19 @@
(map parse-header-line)
into-header)))

(defn- ^"[B" as-byte-array [^String s]
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proton has hex->bytes function, which seems to be equivalent of this function. Is any reason to reinvent it?

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I hadn't noticed that fn. Thank you for pointing that!

@totakke totakke merged commit f2293a4 into master Jul 31, 2017
@totakke totakke deleted the fix/sam-options branch July 31, 2017 07:33
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totakke commented Jul 31, 2017

Thank you :)

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alumi commented Jul 31, 2017

Thank you for the reviewing!

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@alumi @totakke