v1.2.2: Updates to variant_caller parameter and plotting improvements

Author: mdbarnesUCSD

CHANGELOG.md

@@ -6,6 +6,21 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+## [1.2.2] - 2025-07-21
+
+### Added
+- Integrated `pytest` to ensure correct handling of the `variant_caller` parameter.
+
+### Changed
+- Update the standard names for the `variant_caller` parameter
+  - Changed `sanger` to `caveman`
+  - `TCGA` and `standardVC` have been merged into a more flexible `standard` option.
+  - `standard` is now default and parses VAF from 8th and 10th columns of VCF files (`VAF=` or `AF=`).
+
+### Fixed
+- Plotting Stability: Added error handling to skip samples that are invalid and proceed with valid ones.
+- Resolved a potential index out-of-bounds error in the `plot_hist` function.
+
 ## [1.2.1] - 2025-04-02
 
 ### Changed

setup.py

@@ -17,7 +17,7 @@ def readme():
     # 	return(f.read())
 
 
-VERSION = "1.2.1"
+VERSION = "1.2.2"
 
 
 def write_version_py(filename="SigProfilerClusters/version.py"):
@@ -26,7 +26,7 @@ def write_version_py(filename="SigProfilerClusters/version.py"):
 # THIS FILE IS GENERATED FROM SIGPROFILECLUSTERS SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
-Update = 'v1.2.1: Add centromere coordinates for mm39'
+Update = 'v1.2.2: Updates to variant_caller parameter and plotting improvements'
 	
 	"""
     fh = open(filename, "w")