- Json report including in stdout upon successful completion (can be disabled with --no-json)
- Renamed
- Support for paired-end files
- Major under the hood changes to use Noodles for fastq parsing, and Niffler to handle compression (RIP my own code)
- Output a fasta file with
--output-fasta
- Streamline arguments related to compression types/level
- Improved logging
- Code optimisations
- Increased verbosity of outputs to user
--no-compress
flag to output a standard, plaintext fastq file--exclude
to exclude specified reads. Works with--children
and--parents
- Docstrings under the hood
- Fixes to reduce memory usage
- Detect and handle
gz
files or plain files --compression
arg to select compression typezlib-ng
to speed up gzip handling--children
and--parents
to save children and parents based on kraken report
- First release