[DOC] Adding links to enums for class SequenceStream.
[DOC] Greatly improving the documentation of SWIFT and Pigeonhole algos.

Splitting documentation of pattern and finder and also adding
configuration for the *Parameters structs as well as the functions
for disabling SWIFT and Pigeonhole patterns.
[DOC] Improving documentation of ValueSize.
[DOC] Improving documentation of BamIndex.
Merge pull request #210 from holtgrewe/fix_dox_issues

A fix for various dox issues and a bug in the dox system