[INTERNAL] Yara: trying pairing strategies
[INTERNAL] Yara: added getTemplateDeviation() and changed getTemplateLength() return type
[INTERNAL] Yara: refactored pair selector
[INTERNAL] Yara: postponed the selection of a random match
[REVERT] Yara: disabled XA tag
[FIX] Yara: fixed best pair selction criterion
[FIX] Yara: fixed best pair selction criterion
[INTERNAL] Yara: do not explicitly check for unexpected orientations
[INTERNAL] Yara: fill XA tag
[NOP] Yara
[INTERNAL] Yara: count matches by strata
[INTERNAL] Yara: clip suboptimal matches
[FIX] Yara: removed a warning
[FIX] Yara: fill all extra tags for read information
[FEATURE] Yara: added strata-rate option
[INTERNAL] Yara: version 0.9.0
[TEST] Yara: updated test files
[DOC] Improvements to API dox.
Merge pull request #502 from holtgrewe/dox-fixes

[DOC] Improvements to API dox.
Merge pull request #501 from esiragusa/fix/yara/pairedend

Improved paired-end protocol, added mapping by strata.