v0.8.0

Changes

This is a large release with over 600+ commits since the previous one (0.7.1). Much of the work that went into it was enabled by a
Bioinformatics Long-Term Support grant through National Bioinformatics Structure Sweden (NBIS), which is the SciLifeLab Bioinformatics platform.

A majority of the commits was focused on reorganizing the code to make it easier to maintain, to read, to test and to change. This has already paid off in the form of external contributions that would have been more difficult without those changes.

Another focus was on usability and standards compliance: SAM output follows the SAM specification more closely, error messages are better, there is now a --help command-line option, some irrelevant logging output was hidden, and the documentation was updated.

Mapping speed and accuracy remain mostly unaffected in this release, except for one bugfix that increases mapping rate and accuracy at short read lengths (<100 bp). Also, some unintended coverage spikes no longer occur.

Memory usage was decreased due to switching to a modified in-memory representation of the index. For the human genome, for example, RAM usage went from 28 GiB to 21 GiB. The reduction is smaller for more repetitive genomes.

Strobealign also gained the ability to pre-generate an index and save it to disk. As indexing is quite fast, this is not as relevant as it is for other read mappers, but important when processing many small libraries.

Please see the full Changelog.