Increase target–query symmetry with--gapsym and --matsym. #91
Description
In practice it will not affect much the results as they are always very similar, but in theory it will make the alignment parameters easier to explain and display.
One possible criticism is that in the case of some genomes, like mitochondria, there are sequence-biased "heavy" and "light" strands, and that if the genome files are oriented correctly with each other, it may be better to use non-symmetric alignment parameters. But this can always be added as an option later.
Yet, it will require a major version bump as it formally breaks backwards compatibility.