Refactored GenericFile gets:

* Added getchar() to the public interface
* Renamed the gets implementation to _gets_impl and made it protected
* gets is implemented by calling _gets_impl for GenericFile_HDFS and _Blob,
  and by calling stdio's fgets() for GenericFile_stdio
Fixes to enable SNAP to link and build on *nix/Mac.
Generate error messages rather than crashing for invalid keySize/seedLen combos in index build
Compile on Linux
Merge pull request #28 from fnothaft/build-fixes-nix

Build fixes for *nix
removed duplicate definition in Compat.cpp
Merge pull request #29 from amplab/dup-def

removed duplicate definition in Compat.cpp
Merge branch 'dev' of https://github.com/amplab/snap into dev
1.0dev.26: increase secondary result buffer size for paired end aligner
Merge branch 'dev' of https://github.com/amplab/snap into dev
Include readID in error message for running out of secondary results buffer (not that it should happen again)
Linux build
1.0dev.27: Fix SAM->BAM RG bug
Fix comma syntax, which broke when I added single or paired to the @PG line
version to merge back into dev