The denominator of the scoring files (number of variants) will be incorrect in match_variants if we don't keep all variants from the original scoring file in the combined .txt file. This PR adapts combine_scorefiles to account for this.
Still ToDo:
Update match_variants to only flip variants of the scorefile that have not been matched on the forward strand of the target data.
The denominator of the scoring files (number of variants) will be incorrect in match_variants if we don't keep all variants from the original scoring file in the combined .txt file. This PR adapts combine_scorefiles to account for this.
Still ToDo: