0.6.0rc release

sigven · Sep 24, 2020 · 98e617d · 98e617d
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diff --git a/README.md b/README.md
diff --git a/cpsr.py b/cpsr.py
diff --git a/cpsr.toml b/cpsr.toml
@@ -1,14 +1,5 @@
 # CPSR configuration options (TOML).
 
-[secondary_findings]
-## Include variants found in ACMG-recommended list for incidental findings
-## https://www.ncbi.nlm.nih.gov/clinvar/docs/acmg/
-show_sf = true
-
-[maf_limits]
-## choose upper MAF threshold (global) for variants to be included in report
-maf_gnomad = 0.9
-
 [popgen]
 ## choose population source in gnomAD, defaults to the global set
 ## For gnomAD, this can by any of the following values (three-letter codes):
@@ -37,17 +28,13 @@ name = "Custom gene panel"
 version = "1.0"
 url = ""
 
-[classification]
-## for variants with an existing classification in ClinVar, include CPSR classification/score in the output TSV file
-clinvar_cpsr = true
-
 [gwas]
-gwas_hits = true
 ## Required p-value for reporting of GWAS hits
 p_value_min = 5e-6
 
 [other]
 n_vcfanno_proc = 4
 n_vep_forks = 4
 vep_skip_intergenic = false
+#vep_pick_order = "rank,canonical,appris,tsl,biotype,ccds,length,mane"
 vep_pick_order = "canonical,appris,tsl,biotype,ccds,rank,length,mane"
diff --git a/cpsr_views.png b/cpsr_views.png
diff --git a/docs/.DS_Store b/docs/.DS_Store
diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md
@@ -1,6 +1,37 @@
 
 ## CHANGELOG
 
+#### 0.6.0rc - September 24th 2020
+
+- Data updates: ClinVar, GWAS catalog, GENCODE, CIViC, CancerMine, UniProt KB, dbNSFP, Pfam, KEGG, Open Targets Platform, Genomics England PanelApp
+- Software updates: VEP 101
+
+##### Fixed
+  * Duplicated entries in incidental findings
+
+##### Changed
+  * All arguments to `cpsr.py` are now non-positional
+  * Arguments to `cpsr.py` are divided into two groups: _required_ and _optional_
+  * `secondary_findings` is now coined `incidental_findings`
+  * Option ___gwas:gwas_hits___ in CPSR configuration file is now optional argument `--gwas_findings` in `cpsr.py`
+  * Option ___classification:clinvar_cpsr___ in CPSR configuration file is now optional argument `--classify_all` in `cpsr.py`
+  * Option ___maf_imits:maf_gnomad___ in CPSR configuration file is now optional argument `--maf_upper_threshold` in `cpsr.py`
+  * Option ___secondary_findings:show_sf___ in CPSR configuration file is now optional argument `--incidental_findings` in `cpsr.py`
+  * Virtual panels is now displayed through HTML (previously static ggplot plot)
+  * __Settings__ section of report is now divived into three:
+	  * Sample metadata
+	  * Report configuration
+	  * Virtual panel
+  * Classifications of genes as tumor suppressors/oncogenes are now based on a combination of CancerMine citation count and presence in Network of Cancer Genes
+
+##### Added
+  * Missing ACMG criterion for classification of silent and intronic variants outside of splice regions (_ACMG_BP7_)
+  * Missing ACMG criterion for classification of variants in promoter and untranslated regions (_ACMG_BP3_)
+  * Possibility to create custom virtual panel - any combination of genes from panel 0 provided as a single-column text file with argument `--custom_list`
+  * Ensured that non-empty datatables pr. tier (__ClinVar__ and __Non-ClinVar__) are set as the active tab
+  * Improved documentation of variant classification in the __References__ section
+  * DOIs available for all references
+
 #### 0.5.2 - November 18th 2019
 
 ##### Changed

diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst
@@ -1,9 +1,59 @@
 CHANGELOG
 ---------
 
+0.6.0 - September 23rd 2020
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Fixed
+'''''
+
+-  Duplicated entries in incidental findings
+
+Changed
+'''''''
+
+-  All arguments to ``cpsr.py`` is now organized with a ``--`` (no
+   positional arguments)
+-  Arguments to ``cpsr.py`` are divided into two groups: *required* and
+   *optional*
+-  ``secondary_findings`` is now coined ``incidental_findings``
+-  Option **gwas:gwas_hits** in CPSR configuration file is now option
+   ``--gwas_findings`` in ``cpsr.py``
+-  Option **classification:clinvar_cpsr** in CPSR configuration file is
+   now option ``--classify_all`` in ``cpsr.py``
+-  Option **maf_imits:maf_gnomad** in CPSR configuration file is now
+   option ``--maf_upper_threshold`` in ``cpsr.py``
+-  Option **secondary_findings:show_sf** in CPSR configuration file is
+   now option ``--incidental_findings`` in ``cpsr.py``
+-  Virtual panels is now displayed through HTML (previously static
+   ggplot plot)
+-  **Settings** section of report is now divived into three:
+
+   -  Sample metadata
+   -  Report configuration
+   -  Virtual panel
+
+Added
+'''''
+
+-  Missing ACMG criteria for classification of silent and intronic
+   variants outside of splice regions (ACMG_BP7)
+-  Missing ACMG criterion for classification of variants in promoter and
+   untranslated regions (ACMG_BP3)
+-  Possibility to create custom virtual panel - any combination of genes
+   from panel 0 provided as a single-column text file with argument
+   ``--custom_list``
+-  Ensured that non-empty datatables pr. tier (**ClinVar** and
+   **Non-ClinVar**) are set as the active tab
+-  Improved documentation of variant classification in the
+   **References** section
+-  DOIs available for all references
+
 0.5.2 - November 18th 2019
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+.. _changed-1:
+
 Changed
 '''''''
 
@@ -13,6 +63,8 @@ Changed
 -  Moved virtual panel identifier from positional argument to optional
    argument (``--panel_id``) in ``cpsr.py``
 
+.. _added-1:
+
 Added
 '''''
 
@@ -23,6 +75,8 @@ Added
 0.5.1 - October 14th 2019
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 
+.. _fixed-1:
+
 Fixed
 '''''
 
@@ -34,7 +88,7 @@ Fixed
 0.5.0 - September 23rd 2019
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. _fixed-1:
+.. _fixed-2:
 
 Fixed
 '''''
@@ -51,7 +105,7 @@ Fixed
 -  Handling of non-coding variants (synonymous, upstream_variants) in
    the report, no longer excluded
 
-.. _added-1:
+.. _added-2:
 
 Added
 '''''

diff --git a/docs/_build/.DS_Store b/docs/_build/.DS_Store
diff --git a/docs/_build/doctrees/CHANGELOG.doctree b/docs/_build/doctrees/CHANGELOG.doctree
diff --git a/docs/_build/doctrees/about.doctree b/docs/_build/doctrees/about.doctree
diff --git a/docs/_build/doctrees/annotation_resources.doctree b/docs/_build/doctrees/annotation_resources.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/getting_started.doctree b/docs/_build/doctrees/getting_started.doctree
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/doctrees/input.doctree b/docs/_build/doctrees/input.doctree
diff --git a/docs/_build/doctrees/output.doctree b/docs/_build/doctrees/output.doctree
diff --git a/docs/_build/doctrees/variant_classification.doctree b/docs/_build/doctrees/variant_classification.doctree
diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 9086b1f2cd8fac48b33fa82b2101aae5
+config: 430fd7bd5058a69516f266833495f846
 tags: 645f666f9bcd5a90fca523b33c5a78b7