diff --git a/.travis.yml b/.travis.yml index 30a4c5a..9898a08 100644 --- a/.travis.yml +++ b/.travis.yml @@ -6,9 +6,8 @@ python: - '3.9' before_install: - if ! [ -f ./src/GRCh37.tar.gz ]; then - wget ftp://alexandrovlab-ftp.ucsd.edu/pub/tools/SigProfilerMatrixGenerator/GRCh37.tar.gz -P ./src/; - fi + - pip install --upgrade pip setuptools packaging + - if ! [ -f ./src/GRCh37.tar.gz ]; then wget ftp://alexandrovlab-ftp.ucsd.edu/pub/tools/SigProfilerMatrixGenerator/GRCh37.tar.gz -P ./src/; fi install: - pip install .[tests] diff --git a/CHANGELOG.md b/CHANGELOG.md index d357df4..d223287 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), ## [Unreleased] +## [1.2.30] - 2024-10-10 + +### Fixed +- Resolved a bug that caused the code to crash when running with `exome=True` during INDEL processing. The issue was due to incorrect indentation. + ## [1.2.29] - 2024-09-24 ### Added diff --git a/SigProfilerMatrixGenerator/scripts/SigProfilerMatrixGeneratorFunc.py b/SigProfilerMatrixGenerator/scripts/SigProfilerMatrixGeneratorFunc.py index f95358c..2b02238 100644 --- a/SigProfilerMatrixGenerator/scripts/SigProfilerMatrixGeneratorFunc.py +++ b/SigProfilerMatrixGenerator/scripts/SigProfilerMatrixGeneratorFunc.py @@ -2390,6 +2390,10 @@ def SigProfilerMatrixGeneratorFunc( for line in sorted_lines: print("\t".join(line), file=output) + mutation_ID["simple"] = pd.DataFrame( + 0, index=indel_types_simple, columns=samples + ) + mutation_ID["simple"], samples2 = matGen.exome_check( chrom_based, samples, diff --git a/setup.py b/setup.py index 7d58db3..a5af2e1 100644 --- a/setup.py +++ b/setup.py @@ -3,7 +3,7 @@ from setuptools import setup -VERSION = "1.2.29" +VERSION = "1.2.30" # 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 = 'v1.2.29: Resolve issue with non-sorted input and BED files.' +Update = 'v1.2.30: Resolve exome=True issue caused by indentation.' """ fh = open(filename, "w")