Adding 'not hom alt' filter setting

HISTORY.rst

@@ -9,12 +9,14 @@ HEAD (unreleased)
 End-User Summary
 ================
 
+- Adding "not hom. alt." filter setting.
 - Allowing users to easily copy case UUID by icon in case heading.
 - Fixing bug that made the user icon top right disappear.
 
 Full Change List
 ================
 
+- Adding "not hom. alt." filter setting.
 - Improving admin configuration documentation.
 - Extending admin tuning documentation.
 - Allowing users to easily copy case UUID by icon in case heading.

variants/forms.py

@@ -126,6 +126,7 @@ class Meta:
     ("ref", "0/0"),
     ("het", "0/1"),
     ("hom", "1/1"),
+    ("non-hom", "0/0 or 0/1"),
     ("variant", "variant"),
     ("non-variant", "non-variant"),
     ("non-reference", "non-reference"),
@@ -178,6 +179,7 @@ class Meta:
     "ref": ("0/0", "0|0", "0"),
     "het": ("0/1", "0|1", "1/0", "1|0", "1"),
     "hom": ("1/1", "1|1", "1"),
+    "non-hom": ("0/0", "0|0", "0", "0/1", "0|1", "1/0", "1|0", "1"),
     "reference": ("0/0", "0|0", "0"),
     "variant": ("1/0", "1|0", "0/1", "0|1", "1/1", "1|1", "1"),
     "non-variant": ("0/0", "./.", "0"),

variants/templates/variants/filter_form/genotype.html

@@ -30,11 +30,13 @@
               <a class="dropdown-item load-genotype" href="#" data-preset-name="unaffected:any">Unaffected: any</a>
               <a class="dropdown-item load-genotype" href="#" data-preset-name="unaffected:ref">Unaffected: 0/0</a>
               <a class="dropdown-item load-genotype" href="#" data-preset-name="unaffected:het">Unaffected: 0/1</a>
+              <a class="dropdown-item load-genotype" href="#" data-preset-name="unaffected:non-hom">Unaffected: 0/0 or 0/1</a>
               <a class="dropdown-item load-genotype" href="#" data-preset-name="unaffected:non-variant">Unaffected: non-variant</a>
               <a class="dropdown-item load-genotype" href="#" data-preset-name="unaffected:non-reference">Unaffected: non-reference</a>
               <a class="dropdown-item load-genotype" href="#" data-preset-name="affected:any">Affected: any</a>
               <a class="dropdown-item load-genotype" href="#" data-preset-name="affected:het">Affected: 0/1</a>
               <a class="dropdown-item load-genotype" href="#" data-preset-name="affected:hom">Affected: 1/1</a>
+              <a class="dropdown-item load-genotype" href="#" data-preset-name="affected:non-hom">Affected: 0/0 or 0/1</a>
               <a class="dropdown-item load-genotype" href="#" data-preset-name="affected:variant">Affected: variant</a>
               <a class="dropdown-item load-genotype" href="#" data-preset-name="affected:non-reference">Affected: non-reference</a>
             </div>

variants/tests/test_queries.py

@@ -2192,6 +2192,15 @@ def test_genotype_gt_variant_export(self):
     def test_genotype_gt_variant_vcf(self):
         self.run_query(CaseExportVcfQuery, {"%s_gt" % self.patient: "variant"}, 6)
 
+    def test_genotype_gt_non_hom_filter(self):
+        self.run_query(CasePrefetchQuery, {"%s_gt" % self.patient: "non-hom"}, 6)
+
+    def test_genotype_gt_non_hom_export(self):
+        self.run_query(CaseExportTableQuery, {"%s_gt" % self.patient: "non-hom"}, 6)
+
+    def test_genotype_gt_non_hom_vcf(self):
+        self.run_query(CaseExportVcfQuery, {"%s_gt" % self.patient: "non-hom"}, 6)
+
     def test_genotype_gt_non_variant_filter(self):
         self.run_query(CasePrefetchQuery, {"%s_gt" % self.patient: "non-variant"}, 2)