2.0.0

A major release with faster long read decontamination and support for stdin and stdout for both single and paired reads. Interleaved paired reads are now supported via stdin and stdout. A breaking change has been made to hostile clean: the --out-dir argument has been renamed to --output, and now accepts - to write output to stdout rather than files. Decontamination accuracy is unchanged. Thanks to @jannikseidelQBiC, @BioWilko, @dterumalai, @jfy133, @microbemarsh and @charlesfoster for bug reports and suggestions.

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 (#35)
• 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 (#41)
• 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