diff --git a/CHANGELOG.md b/CHANGELOG.md index da1d0c1a..00cc5c32 100644 --- a/CHANGELOG.md +++ b/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. diff --git a/CHEWBBACA/docs/user/getting_started/installation.rst b/CHEWBBACA/docs/user/getting_started/installation.rst index 39688922..4864e9fc 100644 --- a/CHEWBBACA/docs/user/getting_started/installation.rst +++ b/CHEWBBACA/docs/user/getting_started/installation.rst @@ -8,7 +8,7 @@ Install the latest released version using `conda =22.11, and enable the libmamba solver, which might speed up the installation process. @@ -16,7 +16,7 @@ You can also install `mamba ` :: - 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 diff --git a/README.md b/README.md index 79450afc..106d9fa6 100644 --- a/README.md +++ b/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.