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Changelog
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.. Newest changes should be on top.

..  This document is user facing. Please word the changes in such a way
.. that users understand how the changes affect the new version.

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v2.5.2
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* **Important: Please rebuild the HAMLET-data folder when updating to v2.5.2**
* Update variant annotation and inclusion criteria

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v2.5.1
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* Fix a bug with the HAMLET-data folder

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v2.5.0
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* **Important: Please rebuild the HAMLET-data folder when updating to v2.5.0**
* **Deprecate** the ``blacklist`` option in favour of ``known_variants``
* **Deprecate** the ``ref_id_mapping`` option
* **Deprecate** the ``vep_include_consequence`` option
* **Rename** ``filter_criteria`` to ``inclusion_criteria``
* Add option ``min_variant_depth`` to the snv-indels module to specify the
  minimum number of reads to report a variant (default = 2)
* Add support for specifying the frame of variant Criteria
* Add additional annotation file ``known_variants`` to the snv-indels module
* Add the ``--safe`` flag to VEP to ensure there are no hidden errors
* Add support for tabulating gene expression data to the ``hamlet_table.py`` script
* Add support for tabulating cell types to the ``hamlet_table.py`` script
* Add support for tabulating AML subtype prediction to the ``hamlet_table.py`` script
* Simplify the output of the ``hamlet_table.py`` script for variants
* Allow every module to run with the full HAMLET configuration
* The ``report_genes`` file for the fusion module is now optional
* Encode all figures directly into the HTML report
* Clean up intermediate MultiQC files
* Truncate HGVS descriptions longer than 100 characters in the PDF report
* Combine filtering and annotation of variants into a single step
* Update the filter and annotation criteria to include 46 genes
* Reduce the size of the reference files to 35GB
* Update MultiQC to 1.31
* Update cutadapt from 5.0 to 5.1
* Update sequali from 0.12 to 1.0.2
* Update arriba from 2.4.0 to 2.5.1
* Update VEP from 108 (2022) to 115 (2025)

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v2.4.0
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* Fix a bug in the dependency pipeline introduced by Snakemake 8
* Fix a bug with the cell type composition in MultiQC
* Add seAMLess to determine cell type composition
* Add section for gene expression to the PDF report
* Add seAMLess cell type composition to PDF and MultiQC report
* Add Picard Strand Mapping statistics to the MultiQC report
* Add AML subtype prediction with AMLmapR
* Add seAMLess reference files to HAMLET-data
* Add hotspot criteria file to HAMLET-data
* Remove table and figure numbers from the PDF report

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v2.3.3
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* Add script to update HAMLET version (developer)
* Rename the PDF manual in the release bundle
* Add example HAMLET report to the release bundle
* Add example MultiQC report to the release bundle

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v2.3.2
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* Automatically create release notes from Changelog

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v2.3.1
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* **Breaking change**: Removed ``bed_variant_hotspots`` in favor or ``annotation_criteria``
* **Breaking change**: Variants are now filtered using the ``filter_criteria`` file
* **Breaking change**: Add ``mutalyzer_hgvs_parser`` to the conda environment
* **Breaking change**: Update the json output format
* **Breaking change**: Update Snakemake to version 8
* Fix a bug with the Java runtime environment for Picard
* Fix a bug with caching of report assets introduced in snakemake 8
* Fix a bug with structural variants missing effect prediction
* Add an option to specify ``variant_allele_frequency`` for snv-indels
* Speed up VarDict by running with 8 threads
* Speed up VarDict by sorting the call_regions.bed file
* Run VEP with either ``vep_cache`` or just the gtf/fasta files as database
* Update picard from 2.27.4 to 3.3.0
* Update cutadapt from 4.6 to 5.0
* Update sequali from 0.9.1 to 0.12.0
* Update star from 2.7.10b to 2.7.11b
* Update MultiQC to 1.27.1

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v2.2.1
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* **Breaking change**: The ``bed_variant_call_regions`` option has been removed, variants are now
  called for all genes present in the ``gtf`` file.
* **Breaking change**: Add graphviz/``dot`` as a dependency (developer only).
* Fix a rare bug where different modules use the same MultiQC file list.
* Fix a bug with filtering VEP records that contain multiple population.
  frequency records for a single variant.
* Add ability to generate configurations for each module using the
  ``utilities/create-config.py`` script.
* Update the hotspot regions reference file.
* Update the blacklist of known artifacts.
* Remove various superfluous plots from the MultiQC report.
* Add **expression** module
    * Add optional input ``strandedness`` to the sample configuration.
    * Add json output file for the expression module.

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v2.1.3
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* Add ``pysam`` to the conda environment (developer only)
* Add exon number to variant table
* Add chromosomes to fusion table

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v2.1.2
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* Fix a bug with the maximum population frequency, this was accidentally set to
  5% (it is now 1%)

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v2.1.1
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* Fix a bug where VEP removed rare variants

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v2.1.0
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* **Breaking change**: Remove the JSON output for the qc-seq module (this has
  been replaced by a MultiQC report)
* **Breaking change**: Add sample name to STAR counts table * Fix a bug where
  the trimmed FastQ files are not removed when no longer needed
* Automatically remove _STAR temporary folders
* Change PDF report cover image
* Change PDF report to add bookmarks under chapter variant
* Change PDF report to sort the genes of interest alphabetically
* Change PDF report to remove the "Sequencing Results" section (this has been
  replaced by a MultiQC report)
* Replace FastQC with Sequali
* Update Cutadapt to 4.6
* Update MultiQC to 1.22
* Update snakefmt to 0.10.0 (developer only)
* Update black to 24.3.0 (developer only)

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v2.0.5
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* Change PDF report to increase space for the HGVS description in "Results
  Overview" table

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v2.0.4
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* Automatically check the release tag is set correctly

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v2.0.3
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* Fix a bug where long HGVS descriptions make the "Results Overview" table
  overflow the page

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v2.0.2
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* Include the sample name in the final BAM file

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v2.0.1
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* Update version number in HAMLET report

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v2.0.0
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* **Breaking change**: Deprecate option ``fusion-partners``, in favour of
  ``report_genes``, which points to a list of fusion genes to report
* Fix a bug with inconsistent config setting ``blacklist`` in snv-indels
* Fix a bug where unmapped reads are not included in STAR output file
* Replace StarFusion and FusionCatcher with Arriba
* Replace VarScan variant caller with VarDict
* Replace GSNAP aligner with STAR
* Update VEP to 108.2
* Update Picard to 2.27.4
* Update FastQC to 0.11.9
* Update Cutadapt to 4.1
* Change PDF report to remove the run name
* Change PDF report to remove variants plots
* Change PDF report to show allele frequency as a percentage
* Use multiple threads for Cutadapt, and reduce the compression of output files
* Add additional genes of interest
    - SRSF2
    - SF3B1
    - U2AF1
    - BCOR
    - STAG2
    - ZRSR2
    - EZH2
* Filter fusion results based on fusion partners
* Add fusion plots from Arriba
* Add default blacklist with common false-positive variants
* Add support for variant blacklist in VEP hgvsc format
* Add script to generate a configuration file
* Add pipeline to generate reference files
* Add per-module configuration options
* Add support for PEP sample configuration
* Add support for Snakemake 7.8.5
* Use MANE select transcript for all genes