Fix BUG: Issue #143 - #144
Conversation
Codecov Report✅ All modified and coverable lines are covered by tests. 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 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
|
|
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 |
[BUG] FASTQ: Parser fails to parse valid sequences #143
Changes
Seq.groupWhen same_groupwithSeq.chunkBySize 4inFastq.readLinesto correctly parse records by structure .#and;.Description
This PR fixes a critical FASTQ parsing bug where valid sequencing inputs.
[Required] please make sure you checked that