Update INSTALL.TXT

Added information about compilation including the required specification of samtools location
Removing executable
Delete generateCavemanUMNormVCF

Removed executable from github
Update INSTALL.TXT

Minor text edit
Update Makefile

Modified $samtools env variable to use braces so it is interpreted as a variable.
Update Makefile

Added -l pthread as samtools doesn't seem to include it.
Modified Makefile to add relative paths in case -C is used
Removing o files from github source
Removing o files from github source
Adding ignores
Update Makefile

Removed lib and include from includes and lib $SAMTOOLS stuff. If the build is manipulated it can be manually specified
Update Makefile

Moved test out of standard make so we're not trying to test before everything is finished compiling when adding CPUs as part of the  make command.
Update output.c

Fixed format for mutation line output. Format fields didn't match the header FORMAT entries.
Updated output test to cope wioth format line change
Added NOTPARALLEL to test so that the -j option doesn't break make
Removed superfluous test class and added tests for cn_access.c class
Adding defualt cn params for normal and tumour
getter and setter and code to deal with defualt cn settings
Added code to deal with lack of cn file and means to permit default cn settings
removing unrequired file