Some small bugs I have come across

[RhysGillman]

Hi,

Thanks for making this tool! I just wanted to point out a few issues I've come across trying to run PHALCON on my data.

1. The "from src import NNI" and "from src import SPR" lines in maximum_likelihood_tree.py mean that phalcon needs to be run from within the installation directory or else it fails as it can't find the src directory
2. Following on from above, if you get around this by using cd into the installation directory when running, all output files correctly go to the "-o output_prefix" location except for Final clusters inferred.txt, Genotype configuration.tsv, genotype_name_tmp.tsv, tmp_matrix.tsv which are all written straight into the current working directory
3. PHALCON fails if chromosomes aren't "chr" prefixed due to mixing strings and integers in pd.read_csv, causing "DtypeWarning: Columns (0) have mixed types"

So far I have managed to work around these problems by simlinking the src directory to my output directory and temporarily adding chr prefixes to my data.

Cheers,
Rhys