FASTA statistics is not handled properly

esteinig / nanoq

Minimal but speedy quality control for nanopore reads in Rust :bear:

MIT License

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FASTA statistics is not handled properly #21

Closed cgjosephlee closed 2 years ago

cgjosephlee commented 3 years ago

When filtering FASTA or just generating stats I met

thread 'main' panicked at 'index out of bounds: the len is 0 but the index is 18446744073709551615', src/main.rs:678:37
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

But the output FASTA is correct. Should be some errors during generating statistics.

Btw, if we can optionally ignore quality scores, some operations on FASTQ will be much much faster. eg. I only want to filter a FASTQ by read length.

esteinig commented 3 years ago

Thanks so much for stress testing Joseph, much appreciated! Added to the list: bug fix as well as optional q-scores, will also test the option in the benchmarks.

esteinig commented 2 years ago

@cgjosephlee changes implemented (sorry for delay):

main branch now has a stable release fixing the stats bug
-f / --fast mode which ignores quality scores - huge speedup as suggested

esteinig commented 2 years ago

will close for now but feel free to reopen if you run into any issues

thanks for the report and suggestion!