Fix link anchors and other issues in readthedocs

[heuermh]

Some link anchors and other formatting styles were broken after conversion to rst.

File pull requests against this issue for these and other issues with the new documentation hosted at http://adam.readthedocs.io/en/latest/.

E.g.

a known variation database (e.g., dbSNP). {#known-snps}
See candidate generation and realignment. {#known-indels}
While the `transformAlignments <#transformAlignments>`__ command

Regarding Pygments styles, I prefer lovelace and arduino over the default.

[antonkulaga]

You have a small formating issue at http://adam.readthedocs.io/en/latest/architecture/overview/ with \end{itemize}

[antonkulaga]

at http://adam.readthedocs.io/en/latest/api/joins/ it is better to separate right and inner by the line on the pic

[heuermh]

You have a small formating issue at http://adam.readthedocs.io/en/latest/architecture/overview/ with \end{itemize}

Thanks, I think we fixed that in #1827 already.

at http://adam.readthedocs.io/en/latest/api/joins/ it is better to separate right and inner by the line on the pic

Good suggestion, thanks again.

[heuermh]

Fixed by #1827