[FIX-#561] Splits pair_align into multiple translation units to free compilation resources.
[INTERNAL,NOP] Modifies CMakeLists to reduce number of object files build. Fixes some whitespace issues.
[FIX] Disables OBJECT feature which is not supported by cmake versions less than 2.8.8.
[FIX] Fixes compiler issues with set macros from within cmake.
[FIX] Fixes some compiler issues.

Merge branch 'release/fix/561' of https://github.com/rrahn/seqan into release/fix/561

Conflicts:
	apps/pair_align/lib/CMakeLists.txt
Merge branch 'develop' of github.com:seqan/seqan into release/fix/561
[INTERNAL] Some cosmetic changes.
[INTERNAL] Build System: renamed extras tests as seqan_test_xxx
[API] BamIO: renamed nameStore(Cache) as contigNames(Cache) and sequenceLengths as contigLengths
[INTERNAL] Store: updated references to nameStore(Cache) and sequenceLengths
[API,DOX] Giving ProfileChar a larger public interface.
[FIX] Replacing _getMaxIndex by getMaxIndex in some more locations.
[INTERNAL] Store: updated references to nameStore(Cache) and sequenceLengths
[DOC] Manual: small fixes to BamIO tutorial
[FIX] Build System: removed a debug message from FindSeqAn.cmake
[DOC] BamIO: documented contigLengths()
[API,DOC,TEST] BamIO: introduced getContigName() and getContigLength() to get reference sequence name and length from BamAlignmentRecord and BamFile
[DOC] Manual: explained getContigName() and getContigLength() in the BamIO tutorial
Merge pull request #756 from esiragusa/feature/bam_io/contig_names

Renamed BAM I/O contig names, cache, lengths
[DOC] Manual: updated the VcfIO tutorial