scout-browser 4.80__tar.gz → 4.81__tar.gz

{scout-browser-4.80 → scout-browser-4.81}/CHANGELOG.md

@@ -4,6 +4,19 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
+## [4.81]
+### Added
+- Tag for somatic SV IGH-DUX4 detection samtools script
+### Changed
+- Upgraded Bootstrap version in reports from 4.3.1 to 5.1.3
+### Fixed
+- Buttons layout in HPO genes panel on case page
+- Added back old variant rankscore index with different key order to help loading on demo instance
+- Cancer case_report panel-table no longer contains inheritance information
+- Case report pinned variants card now displays info text if all pinned variants are present in causatives
+- Darkmode setting now applies to the comment-box accordion
+- Typo in case report causing `cancer_rank_options is undefined` error
+
 ## [4.80]
 ### Added
 - Support for .d4 files coverage using chanjo2 (Case page sidebar link) with test

{scout-browser-4.80/scout_browser.egg-info → scout-browser-4.81}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.80
+Version: 4.81
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson

scout-browser-4.81/scout/__version__.py

@@ -0,0 +1 @@
+__version__ = "4.81"

{scout-browser-4.80 → scout-browser-4.81}/scout/adapter/mongo/variant.py

@@ -671,7 +671,7 @@ class VariantHandler(VariantLoader):
         result = self.variant_collection.delete_many(query)
         LOG.info("{0} variants deleted".format(result.deleted_count))
 
-    def overlapping(self, variant_obj):
+    def overlapping(self, variant_obj, limit=30):
         """Return overlapping variants.
 
         Look at the genes that a variant overlaps to.
@@ -701,7 +701,7 @@ class VariantHandler(VariantLoader):
         }
         sort_key = [("rank_score", pymongo.DESCENDING)]
         # We collect the 30 most severe overlapping variants
-        variants = self.variant_collection.find(query).sort(sort_key).limit(30)
+        variants = self.variant_collection.find(query).sort(sort_key).limit(limit)
 
         return variants
 

{scout-browser-4.80 → scout-browser-4.81}/scout/constants/__init__.py

@@ -204,6 +204,7 @@ CALLERS = {
         {"id": "ascat", "name": "ASCAT"},
         {"id": "dellycnv", "name": "DellyCNV"},
         {"id": "tiddit", "name": "TIDDIT"},
+        {"id": "igh_dux4", "name": "IGH-DUX4 detection"},
     ],
     "mei": [{"id": "retroseq", "name": "RetroSeq"}],
     "sv": [

{scout-browser-4.80 → scout-browser-4.81}/scout/constants/indexes.py

@@ -61,6 +61,16 @@ INDEXES = {
             name="variantid_caseid_category",
             background=True,
         ),
+        IndexModel(
+            [
+                ("category", ASCENDING),
+                ("case_id", ASCENDING),
+                ("variant_type", ASCENDING),
+                ("rank_score", ASCENDING),
+            ],
+            name="category_caseid_varianttype_rankscore",
+            background=True,
+        ),
         IndexModel(
             [
                 ("case_id", ASCENDING),