Don't use random FASTQ access during hcid check - #115
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Sam-Sims
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May 18, 2026
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minor, non-blocking comment - otherwise LGTM
| for name in hcid_dict[taxid]["mapped_read_ids"] | ||
| } | ||
| read_records = {} | ||
| for name, seq, qual in pyfastx.Fastq(read_file, full_name=False, build_index=False): |
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very minor but could consider an early return here once all needed reads are found e.g all hcid reads were in first 10% of a 5gb fastq file then no need to continue parsing
as I type this though probably not worth it in our use case - so not blocking
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Yeah that's a good idea, let me have a look
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