Fixed single mutation on chromosome issue, adjusted README

README.md

@@ -15,7 +15,7 @@ The purpose of this document is to provide a guide for using the SigProfilerClus
 
 The framework is written in PYTHON, and uses additional SigProfiler packages:
 
-  * PYTHON          version 3.4 or newer
+  * PYTHON          version 3.8 or newer
   * SigProfilerMatrixGenerator (https://github.com/AlexandrovLab/SigProfilerMatrixGenerator)
   * SigProfilerSimulator (https://github.com/AlexandrovLab/SigProfilerSimulator)
 
@@ -123,7 +123,7 @@ Erik N Bergstrom, Mousumy Kundu, Noura Tbeileh, Ludmil B Alexandrov. bioRxiv 202
 
 COPYRIGHT
 
-Copyright (c) 2022, Erik Bergstrom [Alexandrov Lab] All rights reserved.
+Copyright (c) 2023, Erik Bergstrom [Alexandrov Lab] All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 

SigProfilerClusters/SigProfilerClusters.py

@@ -207,7 +207,7 @@ def distance_one_file (sample_path, original_samples, output_path_original, file
 
 			# Calculate the minimum IMDs ensuring that the samples, chromosome, and chromosome arms match
 			# distances = [[int(y[2])-(int(x[2])-2+len(x[3])+len(x[4]))] + x + ['c'] if x[0] == y[0] and int(y[2])<centro_start else [int(y[2])-(int(x[2])-2+len(x[3])+len(x[4]))] + x +['c'] if x[0] == y[0] and centro_end<int(x[2]) else 'aa' if x[0] != y[0] else [int(x[2]) - (int(original_lines[original_lines.index(x)-1][2])-2+len(original_lines[original_lines.index(x)-1][3])+len(original_lines[original_lines.index(x)-1][4]))] + x +['d'] for x,y in zip(original_lines, original_lines[1:])]
-			distances = [[int(y[2])-(int(x[2])-2+len(x[3])+len(x[4]))] + x + ['c'] if x[0] == y[0] and int(y[2])<centro_start else [int(y[2])-(int(x[2])-2+len(x[3])+len(x[4]))] + x +['c'] if x[0] == y[0] and centro_end<int(x[2]) else [abs(int(x[2])) - (int(original_lines[original_lines.index(x)-1][2])-2+len(original_lines[original_lines.index(x)-1][3])+len(original_lines[original_lines.index(x)-1][4]))] + x +['d'] for x,y in zip(original_lines, original_lines[1:])]
+			distances = [[int(y[2])-(int(x[2])-2+len(x[3])+len(x[4]))] + x + ['c'] if x[0] == y[0] and int(y[2])<centro_start else [int(y[2])-(int(x[2])-2+len(x[3])+len(x[4]))] + x +['c'] if x[0] == y[0] and centro_end<int(x[2]) else [abs(int(x[2]) - (int(original_lines[original_lines.index(x)-1][2])-2+len(original_lines[original_lines.index(x)-1][3])+len(original_lines[original_lines.index(x)-1][4])))] + x +['d'] for x,y in zip(original_lines, original_lines[1:])]
 			distances_new = distances[:] + [[distances[-1][0]] + original_lines[-1] + [distances[-1][-1]]]
 			# final_distances = ['bb' if x[1] != y[1] else [min(x[0],y[0])]+y[1:-1]+[x[0]] if x[0] != 'a' and y[0] != 'a' and x[-1] != 'd' else [y[0]] + y[1:-1]+[y[0]] if x[-1] == 'd' and x[0] != 'a' and y[0] != 'a' else x if y[0] == 'a' and x[0] != 'a' else y if x[0] == 'a' and y[0] != 'a' else 'bb' for x,y in zip(distances_new[:], distances_new[1:])]		
 			final_distances = [[x[0]] + x[1:-1]+[x[0]] if x[1] != y[1] and y[1] == 'a' else [min(x[0],y[0])]+y[1:-1]+[x[0]] if x[0] != 'a' and y[0] != 'a' and x[-1] != 'd' else [y[0]] + y[1:-1]+[y[0]] if x[-1] == 'd' and x[0] != 'a' and y[0] != 'a' else x if y[0] == 'a' and x[0] != 'a' else y if x[0] == 'a' and y[0] != 'a' else 'bb' for x,y in zip(distances_new[:], distances_new[1:])]		

setup.py

@@ -15,7 +15,7 @@ def readme():
 	# with open('README.rst') as f:
 	# 	return(f.read())
 
-VERSION = '1.1.0'
+VERSION = '1.1.1'
 
 def write_version_py(filename='SigProfilerClusters/version.py'):
 	# Copied from numpy setup.py