adds option to not compress patterns when merging multiple patternLists
This is useful for specifying site patterns based on separate coding
regions in an alignment. The patterns can not be unique, if we want
to used robust counting methods.
The updates to Patterns do not change the API. I use arrayLists
to make sure the length of weights matches the patternLength, since this
length is used to determine the number of codons downstream. These are
casts into arrays for external consumption.
Some updates to beastgen snuck in here as well. Those changes warn the user if a trait in a tsv file is attributed to a taxon that doesn't exist.
adds option to not compress patterns when merging multiple patternLists
This is useful for specifying site patterns based on separate coding regions in an alignment. The patterns can not be unique, if we want to used robust counting methods.
The updates to Patterns do not change the API. I use arrayLists to make sure the length of weights matches the patternLength, since this length is used to determine the number of codons downstream. These are casts into arrays for external consumption.
Some updates to beastgen snuck in here as well. Those changes warn the user if a trait in a tsv file is attributed to a taxon that doesn't exist.