adding Julia's ambiguous methylation GCG fix

Author: bdoughty

README.md

@@ -2,6 +2,8 @@
 
 ## Authors
 - Ben Doughty @bdoughty
+- Jason Tan @yj-tan
+- Julia Schaepe @juliaschaepe
 
 ## Overview:
 The code here takes paired-end FASTQs from an amplicon SMF experiment and analyzes the single reads for methylation state. It returns both bulk measurements and single-molecule measurements, and the repo has additional code for downstream plotting. There are also scripts in `workflow/scripts` for calling binding (`classify_single_molecule_binding_v2.py`) and fitting the partition function model (`fit_partition_function_model_v3.py`).

workflow/scripts/dSMF-footprints_optional_clustering.py

@@ -271,7 +271,7 @@ def run():
                                     pass
                                 else:
                                     # if GenomeDict[chr][i-1:i+2] == 'CGC':
-                                    if GenomeDict[chr][i-1:i+2] == 'GCG':
+                                    if GenomeDict[chr][i:i+3] == 'GCG':
                                         continue
                                 if readseq[i-pos-1:i-pos+1] == 'GC':
                                     scores[i-start] = 0