Began writing VCF parser into VariantMap.cpp
Merged from prototype.
Added updates to VariantMap.h and fixed compiling bugs
Added debugging code to determine why variants aren't being processed
Error with the for loops leads to 'illegal instruction errors' ; attempting to use while loops instead
version of VCF parser, still trying to get it to work on server
used sscanf instead of '0' magic
added assertion
bugfix: strainRefVec moved outside of while loop
refStrainVec in outer While loop and changed scope variantVec and strainVec
Moved :
Conflicts:
	src/palmapper/VariantMap.cpp
Changed scope of vectors to fix bug
Working version replacing substitutions with insertions and deletions
Insertion/Deletion logic added, more testing on the way
position now relative to first mismatch
Fixed bugs related to position, reference string and reference position
Added SNP processing
Strain names included when inserting variant; fixed int type for SNP processing
Variants without strains aren't added; removed logging messages
Merge branch 'parseVcf' of git.ratschlab.org:software/palmapper into parseVcf