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…Hub Actions - Move performance test scripts from separate location to app/bwa-mem2/ - Update GitHub Actions workflow to reference app/bwa-mem2/test_data - Simplify documentation to reflect new directory structure - Verify workflow syntax is valid and ready for CI/CD
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The Bug
Original Issue: FASTR silently dropped 7-8 reads during conversion due to incorrect chunk boundary detection.
Root Cause:
toFASTR_chunk_processor.py:135usedbuffer.rfind(b"\n@")to find FASTQ record boundaries. This fails because quality scores can contain "@" characters, causing the code to split chunks in the middle of records.Impact:
The Fix
Implemented proper FASTQ record boundary detection in
find_last_fastq_record_boundary(), check detail in file changeApp
The key idea is that using fastr as the plug-and-play tool for one of the most common aligner bwa-mem2. Here, bwa-mem2 will read the read that is streaming by the fastr to fastq command line. This idea can be used for similar tool that can read from stdin.
Performance
I want to test whether the plug-n-play takes more resource to compute. For small dataset, it is fine to use fastr with slight change on running time
CI/CD
The issue is that the fastr lacks of the testing for its functions, I added the small tests for at least verifying the input and output of reads.