Mf snakemake vinayakvsv

[vinayakvsv]

Modifications made to Snakemake workflow

1. mappability, repeats, segdup tracks, reference FASTA, and desired coverage for model now added as parameters on config.yaml for easier modification.
2. fixed an error in how DEL events were being extracted prior to analysis
3. import numpy as np missing from Phase.py

[vinayakvsv]

One other error that I have been running into -- especially during parallel runs of the Snakemake, the ldpaths file in the local conda folder for MF keeps getting deleted during the Phase stage, so the Prediction_SNV rule often throws an error. I am not sure why, but we will need to find a fix for this (likely needs to come from the Anaconda people themselves).