add megadepth for fast genome coverage computation

[borauyar]

Keep deepTools::bamCoverage, but make megadepth the default.

• bamCoverage is too slow, but is well maintained and has a lot of flexible options, plus it doesn't consume much memory.
• megadepth is lightning fast, but it is simple. It doesn't have a lot of the flexible options bamCoverage provides.

So, setting megadepth as the default (most users) and keeping bamCoverage as an alternative could address all issues about flexibility, memory consumption, speed.

[borauyar]

Maybe consider bamToCov instead (seems to be as fast as megadepth with less memory consumption): paper: https://www.biorxiv.org/content/10.1101/2021.11.12.466787v1.abstract?%3Fcollection= code: https://github.com/telatin/bamtocov

[borauyar]

megadepth is added to the pipeline; see https://github.com/BIMSBbioinfo/pigx_rnaseq/commit/557bae8febb631e7aed3487b545ed15e10ba1e25