Fix a bug in reading bgzipped VCF files

[alumi]

Problem

cljam.io.vcf/read-variants throws java.lang.ClassCastException for bgzipped VCF files.

Cause

#180 introduced switching of reader type between java.io.BufferedReader and bgzf4j.BGZFInputStream but did not modify the existing code.

Changes

Switch methods based on the type of reader instance.

Tests

• lein check ✅
• lein test :all ✅
• lein cloverage ✅

[codecov]

Codecov Report

Merging #184 into master will increase coverage by <.01%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #184      +/-   ##
==========================================
+ Coverage   86.47%   86.48%   +<.01%     
==========================================
  Files          75       75              
  Lines        5924     5926       +2     
  Branches      497      497              
==========================================
+ Hits         5123     5125       +2     
  Misses        304      304              
  Partials      497      497

Impacted Files	Coverage Δ
src/cljam/io/vcf.clj	95.74% <ø> (ø)	⬆️
src/cljam/io/vcf/reader.clj	85.93% <100%> (+0.22%)	⬆️

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[niyarin]

LGTM

[athos]

Thanks for the fix! As for the production code change, LGTM👍

As for the test code, it would be nice to have a comment emphasizing that the call to vcf/read-variants at L300 is important to verify this change, in order to prevent someone in the future from accidentally optimizing out that call from the test case. Actually, I didn't get how that test case would verify the change at the first glance 😅

Or alternatively, how about adding one more extra test case that looks like the following, and add a comment noting the above thing to it?

(with-open [v (vcf/reader test-vcf-complex-file)
            g (vcf/reader test-vcf-complex-gz-file)]
  (is (= (vcf/read-variants v)
         (vcf/read-variants g))))

[alumi]

@athos Thanks! I added an extra test case in f4779bb.

[athos]

Thank you for updating! I will merge the changes 💪

[alumi]

Thank you for reviewing @niyarin @athos!!