fix the SequenceKmerReader to accomodate scaffolds and edited from Seb review

Signed-off-by: Maxime Déraspe <maximilien1er@gmail.com>

Reviewed-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
fix whitespaces in SequenceKmerReader.cpp

Signed-off-by: Maxime Déraspe <maximilien1er@gmail.com>
fix coding style from Sebastien review w to be pushed in master branch

Signed-off-by: Maxime Déraspe <maximilien1er@gmail.com>
Merge branch 'patch-kmermatrix' of https://github.com/Zorino/ray.git

Maxime Déraspe implemented a new Surveyor feature that allows one
togenerate a kmer presence/absence matrix in many samples. All of
this runs on top of RayPlatform Actor Playground.

Code reviews:

Link: http://sourceforge.net/p/denovoassembler/mailman/denovoassembler-devel/thread/5319A60A.9030907%40gmail.com/#msg32073722
Link: http://sourceforge.net/p/denovoassembler/mailman/denovoassembler-devel/thread/COL131-W1289FA73F414C2391F6CEAAC8B0%40phx.gbl/#msg32071488
Link: http://sourceforge.net/p/denovoassembler/mailman/denovoassembler-devel/thread/COL131-W128CDD247A6A8D42E04F4CAC8B0%40phx.gbl/#msg32071472
Link: http://sourceforge.net/p/denovoassembler/mailman/denovoassembler-devel/thread/017C19ECDB98F64F99200D83876C44520111A7FC4FE7%40EXCH-MBX-B.ulaval.ca/#msg31999514
Link: http://sourceforge.net/p/denovoassembler/mailman/denovoassembler-devel/thread/COL131-W760CDDC5071A415AB9C5EDAC870%40phx.gbl/#msg32015211
Link: http://sourceforge.net/p/denovoassembler/mailman/denovoassembler-devel/thread/f2d8f53ef133555e36529047f4e95084%40boisvert.info/#msg31993547
Link: http://sourceforge.net/p/denovoassembler/mailman/denovoassembler-devel/thread/5301F42B.6060904%40gmail.com/#msg31988453
Surveyor: avoid creating the Surveyor directory twice

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>