Tagged release

Author: erikbergstrom

README.md

@@ -89,7 +89,7 @@ All errors and progress checkpoints are saved into SigProfilerClusters_[project]
 
 CITATIONS
 
-Bergstrom EN, Luebeck J, Petljak M, Khandekar A, Barnes M, Zhang T, Steele CD, Pillay N, Landi MT, Bafna V, Mischell PS, Harris RS, and Alexandrov LB (2022) Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA. Nature; doi: https://doi.org/10.1038/s41586-022-04398-6
+Erik N Bergstrom, Mousumy Kundu, Noura Tbeileh, Ludmil B Alexandrov. bioRxiv 2022.02.11.480117; doi: https://doi.org/10.1101/2022.02.11.480117
 
 COPYRIGHT
 

SigProfilerClusters/SigProfilerClusters.py

@@ -619,9 +619,9 @@ def analysis (project, genome, contexts, simContext, input_path, output_type='al
 			print("done")
 			print("Subclassification of clustered mutations has finished!")
 
-	# Generates output paths for final results saved as VCF files
-	convertToVCF.generateAllPaths(input_path, contexts)
-	convertToVCF.convertFiles(input_path, contexts, project)
+		# Generates output paths for final results saved as VCF files
+		convertToVCF.generateAllPaths(input_path, contexts)
+		convertToVCF.convertFiles(input_path, contexts, project)
 
 
 	sys.stderr.close()

SigProfilerClusters/version.py

@@ -1,6 +1,6 @@
 
 # THIS FILE IS GENERATED FROM SIGPROFILECLUSTERS SETUP.PY
-short_version = '0.0.32'
-version = '0.0.32'
+short_version = '1.0.0'
+version = '1.0.0'
 
 

setup.py

@@ -15,7 +15,7 @@ def readme():
 	# with open('README.rst') as f:
 	# 	return(f.read())
 
-VERSION = '0.0.32'
+VERSION = '1.0.0'
 
 def write_version_py(filename='SigProfilerClusters/version.py'):
 	# Copied from numpy setup.py