Hostile

Added

- Faster long read decontamination due to automatic caching of MMI indexes
- Support for streaming data input via stdin for both single and interleaved paired FASTQ
- Support for streaming data output via stdout for both single and interleaved paired FASTQ
- Automatic allocation of available cores between alignment and compression tasks
- Support for Illumina CASAVA 1.8+ read headers
- Ability to override remote index repository URL

Changed

- Fixed bug in inverted mode `--invert` with paired reads (42 )
- `--fastq1` and `--fastq2` now accept `-` to read from stdin
- `--out-dir` argument of `hostile clean` renamed to `--output` (or `-o`)
- Now accepts `-` to write reads to stdout rather than files
- Reorganised index-related functionality into `hostile index` subcommands
- `hostile fetch` replaced with `hostile index fetch`
- `--offline` renamed to `--airplane`
- Improved warnings and error messages
- Pins Bowtie2>=2.5.4 and Minimap2>=2.28
- Removed space before `/1` and `/2` when writing paired FASTQ

Added
- Allows cross-platform override of the default index cache directory using the environment variable `HOSTILE_CACHE_DIR`. Previously, overrides using `XDG_DATA_HOME` worked only on Linux. The default remains a platform-specific directory determined by the `platformdirs` library. (32)

Changed
- Dockerfile simplification (suggested by bdklahn). (33)
- Improved usage examples, prompted by Ackia. (34)

Added
- Automatically download and use any standard index by name. Example: `hostile clean --index human-t2t-hla-argos985 --fastq1 reads.fq.gz`. (28)
- Two new standard indexes:
- `human-t2t-hla.rs-viral-202401_ml-phage-202401` (RefSeq viral & Millard Lab phage)
- `human-t2t-hla.argos-bacteria-985_rs-viral-202401_ml-phage-202401` (ARGOS bacteria, RefSeq viral, & Millard Lab phage)
- Improved masking protocol for custom index creation (`hostile mask`):
- Uses `minimap2` with adjusted secondary alignment limits and score thresholds.
- K-merises target genomes into 150mers (10bp step) before alignment. Adds `dnaio` dependency.
- New options for `hostile clean`: `--aligner-args`, `--invert`, and `--offline`.
- Verification of downloaded index checksums in `manifest.json`. (20)
- Adds `version`, `aligner`, and `options` fields to log output.

Changed
- Prevents corruption of empty `fastq.gz` files when no reads remain after decontamination. (24)

Added
- `hostile fetch` subcommand for viewing and downloading prebuilt references.
- Automatic determination of near-ideal alignment thread count based on CPU availability.

Changed
- Renamed `--sort-by-name` to `--reorder`, providing deterministic read order without necessarily sorting.
- Improved decontamination speed for Linux by using Bowtie2’s `--reorder` flag.

Added
- `--aligner-args` option for arbitrary alignment parameter passthrough (e.g., `--aligner-args="--ignore-quals"`).
- `--sort-by-name` option for deterministic output order when using Bowtie2 with multiple threads.

Changed
- Performance improvements for Illumina reads / Bowtie.
- Added a space before `/1` and `/2` when renaming Illumina reads (with `--rename`), enhancing compatibility.
- Improved logging.