Merge pull request #197 from AlexandrovLab/sorting_input_exome

Sorting input exome
AlexandrovLab · Sep 24, 2024 · d17ac81 · d17ac81
2 parents a34ed84 + bb889f0
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,15 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+## [1.2.29] - 2024-09-24
+
+### Added
+- Added sort function to handle non-sorted input and BED files. This posed as an issue for when the BED file was not sorted by chromosome and start position in cases when certain reference genomes were used because of roman numerals and decimal (ie ChrX vs chr10).
+
+### Changed
+- Transcript files were modified to adopt the new sorting standard.
+
+
 ## [1.2.28] - 2024-08-06
 
 ### Added

diff --git a/Dockerfile b/Dockerfile
@@ -5,7 +5,7 @@ FROM python:3.8-slim
 WORKDIR /usr/src/app
 
 # Install SigProfilerMatrixGenerator from PyPI
-RUN pip install SigProfilerMatrixGenerator==1.2.27
+RUN pip install SigProfilerMatrixGenerator==1.2.29
 
 # Create a non-root user named 'spm_user'
 RUN useradd -m -s /bin/bash spm_user

diff --git a/SigProfilerMatrixGenerator/references/chromosomes/exome/GRCh37/GRCh37_exome.interval_list b/SigProfilerMatrixGenerator/references/chromosomes/exome/GRCh37/GRCh37_exome.interval_list
@@ -473062,4 +473062,4 @@ Y	59343020	59343139	+	targeting_new_exome_1.1_content
 22	51237148	51237267	+	bait_302440
 22	51237268	51237387	+	bait_302441
 22	51237388	51237507	+	bait_302442
-22	51237508	51237627	+	bait_302443
+22	51237508	51237627	+	bait_302443