Updated Readme and Changelog.

CHANGELOG.md

@@ -1,12 +1,18 @@
 # Changelog
 
+## 3.3.9 - 2024-07-16
+
+- Fixed an issue related to sequence IDs interpreted by BLAST as PDB chain IDs.
+
+- Fixed an issue related to CDS counting when gene prediction returns no CDSs for one or more inputs.
+
 ## 3.3.8 - 2024-07-02
 
 - Added support for genetic codes 2, 3, 5, 6, 9, 10, 12-16, 21-25 (complete list available [here](https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)). Values passed to `--t`, `--translation-table` are ignored if a training file is used. The CreateSchema, AlleleCall and PrepExternalSchema modules use the genetic code used to create the training file.
 
-- Fixed issue related to data about CDSs close to the contig tips not being available if input FASTA files contain CDSs and `--cds` is used.
+- Fixed an issue related to data about CDSs close to the contig tips not being available if input FASTA files contain CDSs and `--cds` is used.
 
-- Fixed issue in the AlleleCallEvaluator module related to entirely numeric columns.
+- Fixed an issue in the AlleleCallEvaluator module related to entirely numeric columns.
 
 ## 3.3.7 - 2024-06-27
 
@@ -34,7 +40,7 @@
 
 - Added function to check if input files passed to the CreateSchema and AlleleCall modules have unique prefixes longer than 30 characters (the prefix includes everything in the basename before the first `.`). The process prints a message with the list of input files with a prefix longer than 30 characters and exits.
 
-- Fixed issue in the AlleleCall module when running in mode 1 (trying to write the file with the list of invalid CDSs, but the data is not available when running in mode 1).
+- Fixed an issue in the AlleleCall module when running in mode 1 (trying to write the file with the list of invalid CDSs, but the data is not available when running in mode 1).
 
 - Added more tests and improved test scripts.
 

CHEWBBACA/docs/user/getting_started/installation.rst

@@ -8,15 +8,15 @@ Install the latest released version using `conda <https://anaconda.org/bioconda/
 
 ::
 
-	conda create -c bioconda -c conda-forge -n chewie "chewbbaca=3.3.8"
+	conda create -c bioconda -c conda-forge -n chewie "chewbbaca=3.3.9"
 
 If you're having issues installing chewBBACA through conda, please verify that you are using
 conda>=22.11, and enable the libmamba solver, which might speed up the installation process.
 You can also install `mamba <https://mamba.readthedocs.io/en/latest/index.html>`_ and run the following command:
 
 ::
 
-	mamba create -c bioconda -c conda-forge -n chewie "chewbbaca=3.3.8"
+	mamba create -c bioconda -c conda-forge -n chewie "chewbbaca=3.3.9"
 
 .. important::
 	We strongly recommend that users install and use BLAST 2.9.0+ with chewBBACA<=3.3.2. Please open an

README.md

@@ -17,13 +17,11 @@ BLAST Score Ratio as proposed by [Rasko DA et al.](http://bmcbioinformatics.biom
 
 ## News
 
-## 3.3.8 - 2024-07-02
+## 3.3.9 - 2024-07-16
 
-- Added support for genetic codes 2, 3, 5, 6, 9, 10, 12-16, 21-25 (complete list available [here](https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)). Values passed to `--t`, `--translation-table` are ignored if a training file is used. The CreateSchema, AlleleCall and PrepExternalSchema modules use the genetic code used to create the training file.
+- Fixed an issue related to sequence IDs interpreted by BLAST as PDB chain IDs.
 
-- Fixed issue related to data about CDSs close to the contig tips not being available if input FASTA files contain CDSs and `--cds` is used.
-
-- Fixed issue in the AlleleCallEvaluator module related to entirely numeric columns.
+- Fixed an issue related to CDS counting when gene prediction returns no CDSs for one or more inputs.
 
 Check our [Changelog](https://github.com/B-UMMI/chewBBACA/blob/master/CHANGELOG.md) to learn about the latest changes.