From c652546fc1c3facf8bdef09610355a4bc5517e4e Mon Sep 17 00:00:00 2001
From: ebergstr <ebergstr@eng.ucsd.edu>
Date: Tue, 28 Nov 2023 10:12:55 -0800
Subject: [PATCH] Fixed single mutation on chromosome issue, adjusted README

---
 README.md                                  | 4 ++--
 SigProfilerClusters/SigProfilerClusters.py | 2 +-
 setup.py                                   | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 1a4664d..5635768 100755
--- a/README.md
+++ b/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:
 
diff --git a/SigProfilerClusters/SigProfilerClusters.py b/SigProfilerClusters/SigProfilerClusters.py
index a26f7bf..2ad3502 100644
--- a/SigProfilerClusters/SigProfilerClusters.py
+++ b/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:])]		
diff --git a/setup.py b/setup.py
index 6e80c67..f414d81 100644
--- a/setup.py
+++ b/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