Upgrade bgzf to tabix version from gotcloud
Makefile.ext - update dependencies to only recompile source cpp if the library headers change (lib and exe will always be rebuilt)
Parameters - allow PhoneHome to be a legacy parameter
SamReferenceInfo - update operator == to not check the hash since it is unnecessary and could have entries at different indices while containing the same info
Makefile.extlib - update the clean to not error if the files don't exist
BGZF - update to allow append mode
Pileup - improve error message when overrunning the buffer
VCF - add option to update GT field