Merge pull request #200 from AlexandrovLab/SPMG_indel_exome

Fixed the indel issue for exome

.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]

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

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,

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")