Merge pull request #21 from weese/hotfix-versioninfo

[FIX] fixed TR1 includes on Windows
Merge pull request #24 from holtgrewe/hotfix/contrib_vs12

[FEATURE] Including contrib version with support for VS12.
Merge pull request #26 from weese/hotfix-intervaltree

[FIX] fixed bug in interval tree ...
[FIX] Masai: call ArgumentParser setCategory()
Merge pull request #32 from esiragusa/hotfix/masai_category

Fix Masai category
Merge pull request #33 from weese/hotfix-packedstring

fixed resize() for packed and alloc string
Merge pull request #36 from weese/hotfix-versioninfo

[FIX] fixed tr1 and c++11 detection
[FIX] Index Finder: renamed function count() as countOccurrences() - it is ambiguous for gcc
[TEST, INTERNAL] CUDA Index: renamed count() as countOccurrences()
Merge branch 'fix/count' into develop

* fix/count:
  [TEST, INTERNAL] CUDA Index: renamed count() as countOccurrences()
  [FIX] Index Finder: renamed function count() as countOccurrences() - it is ambiguous for gcc
[TEST] FMIndex: removed an old file
[FEATURE] mason_variator: writing out an id for the simulated variants
[NOP] Small comment changes.
[FEATURE] mason_variator: write out variant info

An id can be assigned to the simulated variants and written out to VCF.
The id is also written to the breakpoints TSV file.
Merge pull request #38 from holtgrewe/feature/mason2_update

[FEATURE] mason_variator can now write out variant ids to VCF and breakpoints TSV file
[TEST] FMIndex: tested more specs
[FIX] FMIndex: always initialize first sentinel positions to false during BWT construction
[FIX] FMIndex: initialize first indicator positions in CSA construction
Merge branch 'fix/fm_index_sentinels' into develop

* fix/fm_index_sentinels:
  [FIX] FMIndex: initialize first indicator positions in CSA construction
  [FIX] FMIndex: always initialize first sentinel positions to false during BWT construction
  [TEST] FMIndex: tested more specs
[FEATURE,CLI] Using git version in mason2 programs.