Adding section presets for SV filtration (#616)

Closes: #616 Related-Issue: #616 Projected-Results-Impact: require-revalidation
varfish-org · Aug 25, 2022 · 2737496 · 2737496
1 parent c1de288
commit 2737496
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diff --git a/HISTORY.rst b/HISTORY.rst
@@ -42,6 +42,8 @@ End-User Summary
 - Implement new in-house background database for structural variants (#32).
 - Allow to exclude cases from in-house database through project settings (#579).
 - Adding distinct de novo genotype setting (#562).
+- Adding section presets for SV filtration (#616).
+- Adjusting SV filtration presets (#616).
 
 Full Change List
 ================
@@ -79,6 +81,8 @@ Full Change List
 - Implement new in-house background database for structural variants (#32).
 - Allow to exclude cases from in-house database through project settings (#579).
 - Adding distinct de novo genotype setting (#562).
+- Adding section presets for SV filtration (#616).
+- Adjusting SV filtration presets (#616).
 
 ------
 v1.2.0

diff --git a/svs/forms.py b/svs/forms.py
@@ -414,70 +414,70 @@ def update_quality_fields(self):
                 required=False,
                 initial=None,
                 min_value=0,
-                widget=forms.NumberInput(attrs={"class": "quality-field-gq-min"}),
+                widget=forms.NumberInput(attrs={"class": "quality-field-gq_min"}),
             )
             self.fields[self.get_quality_field_names()[name]["src_min"]] = forms.IntegerField(
                 label="",
                 required=False,
                 initial=None,
                 min_value=0,
-                widget=forms.NumberInput(attrs={"class": "quality-field-src-min"}),
+                widget=forms.NumberInput(attrs={"class": "quality-field-src_min"}),
             )
             self.fields[self.get_quality_field_names()[name]["srv_min"]] = forms.IntegerField(
                 label="",
                 required=False,
-                initial=None,
+                initial=1,
                 min_value=0,
-                widget=forms.NumberInput(attrs={"class": "quality-field-srv-min"}),
+                widget=forms.NumberInput(attrs={"class": "quality-field-srv_min"}),
             )
             self.fields[self.get_quality_field_names()[name]["srv_max"]] = forms.IntegerField(
                 label="",
                 required=False,
                 initial=None,
                 min_value=0,
-                widget=forms.NumberInput(attrs={"class": "quality-field-srv-max"}),
+                widget=forms.NumberInput(attrs={"class": "quality-field-srv_max"}),
             )
             self.fields[self.get_quality_field_names()[name]["pec_min"]] = forms.IntegerField(
                 label="",
                 required=False,
                 initial=None,
                 min_value=0,
-                widget=forms.NumberInput(attrs={"class": "quality-field-pec-min"}),
+                widget=forms.NumberInput(attrs={"class": "quality-field-pec_min"}),
             )
             self.fields[self.get_quality_field_names()[name]["pev_min"]] = forms.IntegerField(
                 label="",
                 required=False,
-                initial=None,
+                initial=1,
                 min_value=0,
-                widget=forms.NumberInput(attrs={"class": "quality-field-pev-min"}),
+                widget=forms.NumberInput(attrs={"class": "quality-field-pev_min"}),
             )
             self.fields[self.get_quality_field_names()[name]["pev_max"]] = forms.IntegerField(
                 label="",
                 required=False,
                 initial=None,
                 min_value=0,
-                widget=forms.NumberInput(attrs={"class": "quality-field-pev-max"}),
+                widget=forms.NumberInput(attrs={"class": "quality-field-pev_max"}),
             )
             self.fields[self.get_quality_field_names()[name]["cov_min"]] = forms.IntegerField(
                 label="",
                 required=False,
-                initial=2,
+                initial=4,
                 min_value=0,
-                widget=forms.NumberInput(attrs={"class": "quality-field-cov-min"}),
+                widget=forms.NumberInput(attrs={"class": "quality-field-cov_min"}),
             )
             self.fields[self.get_quality_field_names()[name]["var_min"]] = forms.IntegerField(
                 label="",
                 required=False,
-                initial=2,
+                initial=4,
                 min_value=0,
-                widget=forms.NumberInput(attrs={"class": "quality-field-var-min"}),
+                widget=forms.NumberInput(attrs={"class": "quality-field-var_min"}),
             )
             self.fields[self.get_quality_field_names()[name]["var_max"]] = forms.IntegerField(
                 label="",
                 required=False,
                 initial=None,
                 min_value=0,
-                widget=forms.NumberInput(attrs={"class": "quality-field-var-max"}),
+                widget=forms.NumberInput(attrs={"class": "quality-field-var_max"}),
             )
             self.fields[self.get_quality_field_names()[name]["fail"]] = forms.CharField(
                 label="",

diff --git a/svs/templates/svs/_filter_form.html b/svs/templates/svs/_filter_form.html
@@ -12,6 +12,47 @@
 
 <form id="filterForm" method="post">{% csrf_token %}
   <div class="card">
+    <div class="card-header row" id="quick-presets">
+      <div class="pr-3" style="height: inherit; vertical-align: middle;">
+        <strong>Quick Presets</strong>
+      </div>
+
+      <div class="dropdown pr-3">
+        <a class="btn btn-sm btn-outline-secondary dropdown-toggle" role="button" id="dropdownFreqs" data-toggle="dropdown">
+          Frequency
+        </a>
+
+        <div class="dropdown-menu" aria-labelledby="dropdownFreqs">
+          <a class="dropdown-item" data-preset="freq-in_house_only">in-house only (default)</a>
+          <a class="dropdown-item" data-preset="freq-relaxed">relaxed</a>
+          <a class="dropdown-item" data-preset="freq-strict">strict</a>
+        </div>
+      </div>
+
+      <div class="dropdown pr-3">
+        <a class="btn btn-sm btn-outline-secondary dropdown-toggle" role="button" id="dropdownVars" data-toggle="dropdown">
+          Variants &amp; Effects
+        </a>
+
+        <div class="dropdown-menu" aria-labelledby="dropdownVars">
+          <a class="dropdown-item" data-preset="vars-all">all</a>
+          <a class="dropdown-item" data-preset="vars-almost_all">almost all (default)</a>
+          <a class="dropdown-item" data-preset="vars-cnv_only">CNV only</a>
+        </div>
+      </div>
+
+      <div class="dropdown">
+        <a class="btn btn-sm btn-outline-secondary dropdown-toggle" role="button" id="dropdownQual" data-toggle="dropdown">
+          Quality
+        </a>
+
+        <div class="dropdown-menu" aria-labelledby="dropdownQual">
+          <a class="dropdown-item" data-preset="quals-all">all</a>
+          <a class="dropdown-item" data-preset="quals-relaxed">relaxed (default)</a>
+          <a class="dropdown-item" data-preset="quals-strict">strict</a>
+        </div>
+      </div>
+    </div>
     <div class="card-header row border-bottom-0 pt-1 pr-1">
       <ul class="nav nav-tabs card-header-tabs">
         <li class="nav-item">
@@ -117,8 +158,15 @@
   </div>
 </form>
 
-{#<script type="text/javascript">#}
-{#  $('[data-toggle-second="tooltip"]').tooltip();#}
-{#  const anchor = window.location.hash;#}
-{#  $(`a[href="${anchor}"]`).tab('show')#}
-{#</script>#}
+<script type="text/javascript">
+  $().ready(
+    // Register functions that apply defaults
+    function () {
+      $("#quick-presets .dropdown-item").each(
+        function () {
+          $(this).click(svQuickPresetClicked)
+        }
+      )
+    }
+  )
+</script>