Merge pull request #224 from AlexandrovLab/development

Development

Author: mdbarnesUCSD

CHANGELOG.md

@@ -6,6 +6,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+## [1.3.3] - 2025-04-16
+
+### Fixed
+- Resolved an issue where ID plots were not generated due to the use of an unrecognized plot type (`96ID`). The correct plot type `IDSB` is now used.
+
+### Deprecated
+- Removed support for **ICGC input format**. The [ICGC Data Portal officially closed](https://www.icgc-argo.org/) in June 2024, and associated example files are no longer accessible. Since the format is no longer actively maintained or distributed, and unresolved issues remained (see [#158](https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/issues/158), [#159](https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/issues/159)), support has been deprecated to reduce maintenance burden and avoid user confusion.
+
 ## [1.3.2] - 2025-03-13
 
 ### Fixed

README.md

@@ -89,7 +89,7 @@ View the table below for the full list of parameters.
 
 **INPUT FILE FORMAT**
 
-This tool currently supports maf, vcf, simple text file, and ICGC formats. The user must provide variant data adhering to one of these four formats. If the user’s files are in vcf format, each sample must be saved as a separate files.
+This tool currently supports maf, vcf, and simple text file. The user must provide variant data adhering to one of these three formats. If the user’s files are in vcf format, each sample must be saved as a separate files.
 
 
 **OUTPUT FILE STRUCTURE**

SigProfilerMatrixGenerator/scripts/MutationMatrixGenerator.py

@@ -3798,7 +3798,7 @@ def matrix_generator_INDEL(
                 output_file_matrix_tsb,
                 output_path,
                 file_name,
-                "96ID",
+                "IDSB",
                 False,
                 volume=volume,
             )

SigProfilerMatrixGenerator/scripts/SigProfilerMatrixGeneratorFunc.py

@@ -1343,8 +1343,9 @@ def SigProfilerMatrixGeneratorFunc(
                 project, vcf_path, reference_genome, output_path, ncbi_chrom, log_file
             )
         elif file_extension == "tsv":
-            snv, indel, skipped, samples = convertIn.convertICGC(
-                project, vcf_path, reference_genome, output_path, ncbi_chrom, log_file
+            print("ICGC format (.tsv) is no longer supported. Please convert your file to .vcf, .maf, or .txt.")
+            raise ValueError(
+                "ICGC format (.tsv) is no longer supported. Please convert your file to .vcf, .maf, or .txt."
             )
         else:
             print("File format not supported")