Some boolean parameters need to be renamed to have the default value as false

Rename the following boolean parameters in order to be able to set default values as false and keep default behaviour:

WEIGHTED_COUNT -> DISABLE_MULTIMAP_WEIGHTING
SAM_MATES_ONLY -> IGNORE_SAM_PAIRING_INFORMATION
NO_FILE_CHECK -> DISABLE_FILE_CHECK
DECONVOLUTE -> DISABLE_DECONVOLUTION