New features

Uses baseline categories recommended by the creators of ldsc. This should lead to more accurate enrichment values and also better p-values.
- baseline categories add a lot of noise to the enrichment heatmaps, so separate heatmaps are made solely for the annotations that the user can control (state assignments etc.)
Bedtools is now used to find the windows that a SNP falls into. This is techinically faster, but the speed is largely cancelled out from the excessive I/O usage. Speed ups will be significant if a high number of states/marks are used in analysis.
Epigenetic marks (from ChromHMM binary files) are now factored into the annot files and therefore partitioned heritability
Due to the high number of traits and annotations being considered. Two metrics have been added to p-value bar plots
- Bonferroni significance (this doesn't take into account factors out of your control, mainly the number of annotations in the baseline annot files)
- FDR correction (uses the BH method)

Other changes

Split script 7 into two scripts (one for reference LDSCores, the other for heritability)
- This was to avoid memory issues that came from including the baseline annotations
Removed --gwas (-g) flag for ldsc scripts. These caused lots of problems

Fix multiple bugs that could cause partitioned heritability to break (python related and glob related bugs)
Updated the logic