* Fasta files are automatically indexed if that's not already done.
* The Keep* options were changed to keep* (e.g., --KeepCpG is now --keepCpG).
* --ignoreDupes is now --keepDupes
* Added --noSingleton and --noDiscordant to ignore singleton and discordant alignments.
* We now check to ensure that at least one methylation context is being output.