What's new in 0.19.2

Bug Fixes

Fixed a bug where single-end reads would be discarded using --sep-strands.
Fixed bugs causing the relate step to fail with a mixture of two-mate and one-mate paired-end reads (possible with Bowtie2 mixed mode, --bt2-mixed).
Updated the read counter and the SAM parser to handle mixed mode properly; added unit tests.
Implemented a more robust method of creating temporary directories.
Changed the FASTA parser and writer so that they raise errors if any name/sequence is invalid, rather than skipping invalid sequences and returning the rest, to avoid a potential bug where if two references had the same name, it could be unclear which sequence would actually be used (which has become more of a concern with --sep-strand because minus-strand references can be created automatically).

Full Changelog: v0.19.1...v0.19.2