revert a false bug fix

hiruna72 · Jan 15, 2024 · 2c8c70b · 2c8c70b
1 parent 1af3cac
commit 2c8c70b
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Showing 2 changed files with 1 addition and 13 deletions.
diff --git a/src/plot.py b/src/plot.py
@@ -679,10 +679,6 @@ def run(args):
 
                 signal_tuple, region_tuple, sig_algn_dic, fasta_seq = plot_utils.adjust_before_plotting(seq_len, signal_tuple, region_tuple, sig_algn_dic, fasta_seq)
 
-                # if args.auto_base_shift:
-                #     draw_data["base_shift"] = plot_utils.calculate_base_shift(signal_tuple[2], fasta_seq, sig_algn_dic['ss'], args)
-                #     print("automatically calculated base_shift: {}".format(draw_data["base_shift"]))
-
                 if draw_data["base_shift"] < 0:
                     abs_base_shift = abs(draw_data["base_shift"])
                     x = signal_tuple[0]
@@ -908,10 +904,6 @@ def run(args):
             # print(fasta_seq)
             signal_tuple, region_tuple, sig_algn_dic, fasta_seq = plot_utils.adjust_before_plotting(ref_seq_len, signal_tuple, region_tuple, sig_algn_dic, fasta_seq)
 
-            # if args.auto_base_shift:
-            #     draw_data["base_shift"] = plot_utils.calculate_base_shift(signal_tuple[2], fasta_seq, sig_algn_dic['ss'], args)
-            #     print("automatically calculated base_shift: {}".format(draw_data["base_shift"]))
-
             if draw_data["base_shift"] < 0:
                 abs_base_shift = abs(draw_data["base_shift"])
                 x = signal_tuple[0]
@@ -1130,10 +1122,6 @@ def run(args):
 
             signal_tuple, region_tuple, sig_algn_dic, fasta_seq = plot_utils.adjust_before_plotting(ref_seq_len, signal_tuple, region_tuple, sig_algn_dic, fasta_seq)
 
-            # if args.auto_base_shift:
-            #     draw_data["base_shift"] = plot_utils.calculate_base_shift(signal_tuple[2], fasta_seq, sig_algn_dic['ss'], args)
-            #     print("automatically calculated base_shift: {}".format(draw_data["base_shift"]))
-
             if draw_data["base_shift"] < 0:
                 abs_base_shift = abs(draw_data["base_shift"])
                 x = signal_tuple[0]

diff --git a/src/plot_pileup.py b/src/plot_pileup.py
@@ -372,7 +372,7 @@ def run(args):
     draw_data["bed_labels"] = args.print_bed_labels
 
     if args.profile == "":
-        draw_data["base_shift"] = PLOT_BASE_SHIFT
+        draw_data["base_shift"] = args.base_shift
     else:
         if args.plot_reverse:
             draw_data["base_shift"] = plot_utils.search_for_profile_base_shift(args.profile)[1]