Merge pull request #203 from AlexandrovLab/i201

I201

CHANGELOG.md

@@ -6,6 +6,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+## [1.2.31] - 2024-11-6
+
+### Fixed
+- Resolved a bug where DBS and ID matrices were not being returned due to an indentation issue when the parameter 'chrom_based' was set as True.
+
+### Notice
+- Python 3.8 support will be phased out in future updates as we align with Python's ongoing release cycle. Users on Python 3.8 are encouraged to consider upgrading to Python 3.9 or newer.
+
 ## [1.2.30] - 2024-10-10
 
 ### Fixed

SigProfilerMatrixGenerator/scripts/SigProfilerMatrixGeneratorFunc.py

@@ -2075,7 +2075,7 @@ def SigProfilerMatrixGeneratorFunc(
                             plot,
                             volume=volume,
                         )
-                        matrices["DINUC"] = dinuc_mat
+                matrices["DINUC"] = dinuc_mat
 
         else:
             for file in vcf_files:
@@ -2835,7 +2835,7 @@ def SigProfilerMatrixGeneratorFunc(
                     plot,
                     volume=volume,
                 )
-                matrices["ID"] = mutation_ID["ID"].iloc[0:83, :]
+            matrices["ID"] = mutation_ID["ID"].iloc[0:83, :]
 
         if i == 1:
             shutil.rmtree(output_matrix + "temp/")

setup.py

@@ -3,7 +3,7 @@
 
 from setuptools import setup
 
-VERSION = "1.2.30"
+VERSION = "1.2.31"
 
 # remove the dist folder first if exists
 if os.path.exists("dist"):
@@ -23,7 +23,7 @@ def write_version_py(filename="SigProfilerMatrixGenerator/version.py"):
 # THIS FILE IS GENERATED FROM SIGPROFILEMATRIXGENERATOR SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
-Update = 'v1.2.30: Resolve exome=True issue caused by indentation.'
+Update = 'v1.2.31: Resolve issue of ID and DBS matrices not being returned in the output matrices when chrom_based is set to True.'
 
 	"""
     fh = open(filename, "w")