Remove or add back non-covered sites from compressed counts files

[andrewdavidsmith]

• Adding the covered command to filter counts files for only covered sites. This is needed because rezipping using the bgzf api somehow gets better compression than defaults for gzip
• smithlab_cpp: udpating submodule
• recovered.cpp: adding the recovered.cpp file for adding the missing sites back to the file
• Makefile.am: adding the recovered.cpp file for the recovered command
• dnmtools.cpp: adding the recovered command
• recovered.cpp: removing an unused variable to silence warnings