gzip-compression functionality for reading and writing FASTQ and FASTA files.#107
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ssnn-airr merged 8 commits intoimmcantation:masterfrom Jan 14, 2026
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bin/AlignSets.py
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| # For explicit output files, check if gzip is needed | ||
| if out_args.get('gzip_output', False) and not out_file.endswith('.gz'): | ||
| out_file = out_file + '.gz' | ||
| from presto.IO import openFile |
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For consistency, I will move this and other imports to the top of the files.
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Merged. I made some changes and added some tests to IO and ci.yml, and removed not needed tests and files.
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This pull request adds gzip-compression functionality using the standard python library
gzip. Compression is executed (or not) according to file name suffix.Unit tests
Unit tests and toy files have been added.
Help strings
All help strings have been updated to reflect this new capability.
Compression control of autogenerated file names
The default format continues to be uncompressed FASTQ. That means that programmes (like PairSeq.py) writing files to user-defined directories would still write to .fastq unless the user also specifies
--gzip-output, in which case the files will be compressed (.fastq.gz)Consistent suffix abbreviation
If an input files is .fastq (or .fastq.gz), its auto-generated suffix will be .fastq (or .fastq.gz).
If an input files is .fq (or .fq.gz), its auto-generated suffix will be .fq (or .fq.gz).