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BioJulia / FASTX.jl

Parse and process FASTA and FASTQ formatted files of biological sequences.
https://biojulia.dev
MIT License
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Fix FASTQ line counting bug #39

Closed jakobnissen closed 3 years ago

jakobnissen commented 3 years ago

MWE:

using FASTX
s = join(collect("@A+J@A/J"), '\n')
println(collect(FASTQ.Reader(IOBuffer(s))))

Output:

ERROR: LoadError: ArgumentError: malformed FASTQ file at line 6

But the mistake is actually on line 7, not line 6. The problem was a previous change I had made in #28 , where I accidentally had the @escape action before the @countline action, so the latter was never taken.

codecov[bot] commented 3 years ago

Codecov Report

Merging #39 (7c80fb9) into master (b0c50a4) will not change coverage. The diff coverage is 100.00%.

Impacted file tree graph

@@           Coverage Diff           @@
##           master      #39   +/-   ##
=======================================
  Coverage   87.85%   87.85%           
=======================================
  Files          14       14           
  Lines         634      634           
=======================================
  Hits          557      557           
  Misses         77       77
Flag Coverage Δ
unittests 87.85% <100.00%> (ø)

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Impacted Files Coverage Δ
src/fastq/readrecord.jl 87.69% <100.00%> (ø)

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