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Fix BUG: Issue #143 - #144

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Ahmottie wants to merge 1 commit into
BioFSharp:mainfrom
Ahmottie:fix-fastq
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Fix BUG: Issue #143#144
Ahmottie wants to merge 1 commit into
BioFSharp:mainfrom
Ahmottie:fix-fastq

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@Ahmottie

@Ahmottie Ahmottie commented Aug 31, 2026

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[BUG] FASTQ: Parser fails to parse valid sequences #143

Changes

  • Replaced Seq.groupWhen same_group with Seq.chunkBySize 4 in Fastq.readLines to correctly parse records by structure .
  • Removed the incorrect code which filtered out # and ; .

Description

This PR fixes a critical FASTQ parsing bug where valid sequencing inputs.

[Required] please make sure you checked that

  • The project builds without problems on your machine

@codecov

codecov Bot commented Sep 2, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 50.68%. Comparing base (682ac73) to head (6cc4506).

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #144   +/-   ##
=======================================
  Coverage   50.68%   50.68%           
=======================================
  Files         112      112           
  Lines        8428     8428           
  Branches      879      878    -1     
=======================================
  Hits         4272     4272           
  Misses       4155     4155           
  Partials        1        1           

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@kMutagene

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Hi @Ahmottie

Thanks for taking the time for reporting issues and being available to actually fix something in this lib.

This is a reasonable minimal implementation. A more general parser would use a small state machine: accumulate sequence until +, then accumulate quality characters until their count equals the sequence length. This also handles wrapped FASTQ safely.

Can i kindly request a regression test from you? you basically already demonstrated an input that will trigger this bug, so a small unit test that passes with that input would be greatly appreciated

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2 participants