Debug output removed
Libs from AMD APP SDK added to project.
New Version
Fixed parsing reads without quality values from SAM file.
Added seqan-1.4.1 to lib/
Global alignment with affine gap penalties added.
New parameter --affine
New parameter --affine
Filter duplicated alignments. 
Only for output. Duplicated alignments can still influence MQ!
Changed score bonus/penalty parameters
Added --affine
Changed -m/--mode to -l/--local and -e/--end-to-end
Corrected help text for -R
Min score of 0
Report number of properly paired reads and estimated insert size after
mapping.
Reverse sequences with 0x10 flag when reading from SAM files!
Reverse sequences with 0x10 flag when reading from SAM files!
/1 and /2 are now removed from read names to ensure proper paired end
SAM output.
Typo
Small adjustment to identity threshold.
Additional debug code. Print CMRs as bed file.
Version
Merge branch 'affine-seqan' into dev

Conflicts:
	src/config/Options.h