Joseph Crispell

R Session Aborted

2

I think the `R Session Aborted` error is caused by `homoplasyFinder` hanging after an error has been introduced. See the image below, I introduced an error by sending the wrong...

At the moment declaring boolean arrays of length 4 to store state presence at lines 508 and 511 in [ConsistencyIndex.java](https://github.com/JosephCrispell/Java/blob/master/HomoplasyFinder/src/homoplasyFinder/ConsistencyIndex.java). Should use the `comparePossibleStatesOfTwoSubNodes()` function's `nStatesPerSite` parameter instead of hard...

Ideally I would like to use homoplasyFinder to identify convergent Amino Acid changes as well as nucleotide changes. This is one goal of the code overhaul that is in progress....

Output inconsistent sites as VCF file

3

An important enhancement pointed out by [flashton2003](https://github.com/flashton2003). Thanks! Include option in `homoplasyFinder` to export the `consistencyIndexReport_DATE.txt` file in a VCF file format. The VCF file can then easily be run...