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Added shortcut --long-reads to set suitable parameters for long read alignment: --range-culling (query range-based hit culling), --top 10 (locally report hits within 10% of the best alignment score) and -F 15 (use frameshift alignment mode).
Fixed a performance issue for very long query sequences. The "longs reads" mode can now efficiently align query sequences that are several megabases in length.
Added support for using a FASTA file instead of a Diamond database as the --db parameter in alignment workflows. Note that this incurs substantial overhead and should not be used for large databases.
Fixed an issue that could cause too high memory usage.
Added output field qqual to print query FASTQ quality values to the tabular format.
Changed license to GPL.
Raised compiler requirement to GCC 4.6.
Added option to use the DAA output format for diamond view.
Added CL (command line) and VN (version) fields to the @pg SAM format header line.