Added kmer counting tool to ngs-utils
Conflicts:
	src/SequenceProvider.cpp
	src/SequenceProvider.h
	src/Version.h
	src/config/Config.cpp
ARGOS integration
ARGOS integration
Merge branch 'dev-kmertool-merge' into dev

Conflicts:
	src/AlignmentBuffer.h
	src/config/Config.cpp
ARGOS integration
Debug logger
Debug logger
Debug logger
ngs-utils: count-reads added
Merge branch 'dev' of file:////software/git/repositories/NextGenMap into
dev

Conflicts:
	utils/CMakeLists.txt
	utils/main.cpp
Corrected interleave function in ngm-utils.
Added SAMRecords to NGM to store and handle mapped reads
Added Counting methods for mapped reads in ngm-utils.
Added fasta reformatting
Started Verbose -> Debug
Started Verbose -> Debug
ARGOS: fixed converting sequence location
ARGOS: score filter
ngm-core-debug and ngm-log added
debug
Merge branch 'master' into dev12-master11-merge

Conflicts:
	src/AlignmentBuffer.cpp
	src/AlignmentBuffer.h
	src/NGM_main.cpp
	src/ScoreBuffer.cpp
	src/config/Config.cpp
	src/writer/GenericReadWriter.h
	utils/CMakeLists.txt
--argos parameter added