scout-browser 4.91__tar.gz → 4.91.2__tar.gz

{scout-browser-4.91 → scout-browser-4.91.2}/CHANGELOG.md

@@ -4,6 +4,23 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
+## [4.91.2]
+### Fixed
+- Stranger TRGT parsing of `.` in `FORMAT.MC`
+- Parse ClinVar low-penetrance info and display it alongside Pathogenic and likely pathogenic on SNVs pages
+- Gene panel indexes to reflect the indexes used in production database
+- Panel version check while editing the genes of a panel
+- Display unknown filter tags as "danger" marked badges
+- Open WTS variantS SNVs and SVs in new tabs
+- PanelApp panels update documentation to reflect the latest changes in the command line
+- Display panel IDs alongside panel display names on gene panels page
+- Just one `Hide removed panels` checkbox for all panels on gene panels page
+- Variant filters redecoration from multiple classifications crash on general case report
+
+## [4.91.1]
+### Fixed
+- Update IGV.js to v3.1.0
+- Columns/headings on SV variantS shifted
 
 ## [4.91]
 ### Added

{scout-browser-4.91/scout_browser.egg-info → scout-browser-4.91.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.91
+Version: 4.91.2
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson

scout-browser-4.91.2/scout/__version__.py

@@ -0,0 +1 @@
+__version__ = "4.91.2"

{scout-browser-4.91 → scout-browser-4.91.2}/scout/adapter/mongo/panel.py

@@ -501,7 +501,7 @@ class PanelHandler:
         new_panel["version"] = float(version)
 
         # Update same version or create new version
-        if version == panel_obj["version"]:
+        if new_panel["version"] == panel_obj["version"]:
             result = self.panel_collection.find_one_and_replace(
                 {"_id": panel_obj["_id"]}, new_panel, return_document=pymongo.ReturnDocument.AFTER
             )

{scout-browser-4.91 → scout-browser-4.91.2}/scout/build/variant/clnsig.py

@@ -1,18 +1,13 @@
 import logging
+
 from scout.constants import REV_CLINSIG_MAP
 
 LOG = logging.getLogger(__name__)
 
 
-def build_clnsig(clnsig_info):
-    """Prepare clnsig information for database
-
-    Args:
-        clnsig_info(dict): Parsed information from clinvar annotation
+def build_clnsig(clnsig_info: dict) -> dict:
+    """Prepare clnsig information for database."""
 
-    Returns:
-        clnsig_obj(dict): Converted and prepared for database
-    """
     value = clnsig_info["value"]
     if value not in REV_CLINSIG_MAP:
         LOG.warning("Clinsig value %s does not have an internal representation", value)
@@ -24,4 +19,7 @@ def build_clnsig(clnsig_info):
         revstat=clnsig_info.get("revstat"),
     )
 
+    if isinstance(value, str) and "low_penetrance" in value:
+        clnsig_obj["low_penetrance"] = True
+
     return clnsig_obj

{scout-browser-4.91 → scout-browser-4.91.2}/scout/constants/clnsig.py

@@ -33,7 +33,9 @@ REV_CLINSIG_MAP = {
     "conflicting_classifications_of_pathogenicity": 8,
     "uncertain_significance": 0,
     "likely_pathogenic": 4,
+    "likely_pathogenic,low_penetrance": 4,
     "pathogenic": 5,
+    "pathogenic,low_penetrance": 5,
     # These are here so that the parsing function will work with the older clinvar format
     # Where significance where annotated with numbers
     0: 0,

{scout-browser-4.91 → scout-browser-4.91.2}/scout/constants/indexes.py

@@ -8,6 +8,17 @@ INDEXES = {
             name="genes",
         )
     ],
+    "gene_panel": [
+        IndexModel(
+            [("panel_name", ASCENDING), ("version", ASCENDING)],
+            name="panel_name_version",
+            unique=True,
+        ),
+        IndexModel(
+            [("genes.hgnc_id", ASCENDING)],
+            name="genes.hgnc_id",
+        ),
+    ],
     "hgnc_gene": [
         IndexModel(
             [("build", ASCENDING), ("chromosome", ASCENDING)],

scout-browser-4.91.2/scout/parse/variant/callers.py

@@ -0,0 +1,143 @@
+import logging
+from typing import Optional
+
+import cyvcf2
+
+from scout.constants import CALLERS
+
+LOG = logging.getLogger(__name__)
+
+PASS_STATUS = "Pass"
+FILTERED_STATUS = "Filtered"
+
+
+def parse_callers(variant: cyvcf2.Variant, category: str = "snv") -> dict:
+    """Parse how the different variant callers have performed
+
+    Caller information can be passed in one of three ways, in order of priority:
+    1. If a FOUND_IN tag (comma separated) is found, callers listed will be marked Pass
+    2. If a svdb_origin tag (pipe separated) is found, callers listed will be marked Pass
+    3. If a set tag (dash separated, GATK CombineVariants) is found, callers will be marked Pass or Filtered accordingly
+
+    If the FILTER status is not PASS (e.g. None - cyvcf2 FILTER is None if VCF file column FILTER is "PASS"),
+    in all of these cases, if a single caller is found, the caller status is set to the filter status.
+    If there is more than one caller, we can't quite tell which one is which, so all caller statuses will be "Filtered" instead.
+
+    Args:
+        variant (cyvcf2.Variant): A variant object
+
+    Returns:
+        callers (dict): A dictionary on the format
+        {'gatk': <filter>,'freebayes': <filter>,'samtools': <filter>}
+    """
+    FILTERED = "Filtered - {}"
+
+    relevant_callers = CALLERS[category]
+    callers = {caller["id"]: None for caller in relevant_callers}
+    callers_keys = set(callers.keys())
+
+    def get_callers_from_found_in(info_found_in: str, filter_status: Optional[str]) -> dict:
+        """If a FOUND_IN tag (comma separated) is found, callers listed will be marked Pass.
+        In case of a FILTER status, also set the caller status for a single caller to 'Filtered - status'.
+        If more than one caller, and FILTER status, we cant really tell which said what, and all will be
+        "Filtered".
+        """
+        found_ins: list = info_found_in.split(",")
+
+        call_status = PASS_STATUS
+        if filter_status is not None:
+            call_status = (
+                FILTERED.format(filter_status.replace(";", " - "))
+                if len(found_ins) == 1
+                else FILTERED_STATUS
+            )
+
+        for found_in in found_ins:
+            called_by = found_in.split("|")[0]
+            if called_by in callers_keys:
+                callers[called_by] = call_status
+        return callers
+
+    info_found_in: str = variant.INFO.get("FOUND_IN")
+    if info_found_in:
+        return get_callers_from_found_in(info_found_in, variant.FILTER)
+
+    def get_callers_from_svdb_origin(svdb_origin: str, filter_status: Optional[str]) -> dict:
+        """If a svdb_origin tag (pipe separated) is found, callers listed will be marked Pass.
+        In case of a FILTER status, also set the caller status for a single caller to 'Filtered - status'.
+        """
+        svdb_callers: list = svdb_origin.split("|")
+
+        call_status = PASS_STATUS
+        if filter_status is not None:
+            call_status = (
+                FILTERED.format(filter_status.replace(";", " - "))
+                if len(svdb_callers) == 1
+                else FILTERED_STATUS
+            )
+
+        for called_by in svdb_callers:
+            if called_by in callers_keys:
+                callers[called_by] = call_status
+        return callers
+
+    svdb_origin = variant.INFO.get("svdb_origin")
+    if svdb_origin:
+        return get_callers_from_svdb_origin(svdb_origin, variant.FILTER)
+
+    def get_callers_from_set(info_set: str, filter_status: str) -> dict:
+        """
+        If the FILTER status is not PASS (e.g. None - cyvcf2 FILTER is None if VCF file column FILTER is "PASS"),
+        in all of these cases, if a single caller is found, the "Pass" status is replaced with variant filter
+            status. If there is more than one caller, we can't quite tell which one is which, so all will be "Filtered"
+            without explicit status instead.
+
+        """
+
+        calls = info_set.split("-")
+
+        call_status = PASS_STATUS
+        if filter_status is not None:
+            call_status = (
+                FILTERED.format(filter_status.replace(";", " - "))
+                if len(calls) == 1
+                else FILTERED_STATUS
+            )
+
+        for call in calls:
+            if call == "FilteredInAll":
+                for caller in callers:
+                    callers[caller] = FILTERED_STATUS
+                return callers
+            if call == "Intersection":
+                for caller in callers:
+                    callers[caller] = PASS_STATUS
+                return callers
+            if "filterIn" in call:
+                if "Filtered" not in call_status:
+                    call_status = FILTERED_STATUS
+                for caller in callers:
+                    if caller in call:
+                        callers[caller] = call_status
+            elif call in callers_keys:
+                callers[call] = PASS_STATUS
+        return callers
+
+    info_set = variant.INFO.get("set")
+    if info_set:
+        return get_callers_from_set(info_set, variant.FILTER)
+
+    def get_callers_gatk_snv_fallback(filter_status: Optional[str]):
+        """As a final fallback, to accommodate a version range of MIP where no SNV caller was set for GATK,
+        if this is an SNV variant, and no other call was found, set as if it was a GATK call with Pass or filter status.
+        """
+        filter_status_default = "Pass"
+        if filter_status is not None:
+            filter_status_default = FILTERED.format(filter_status.replace(";", " - "))
+        callers["gatk"] = filter_status_default
+        return callers
+
+    if category == "snv":
+        return get_callers_gatk_snv_fallback(variant.FILTER)
+
+    return callers

{scout-browser-4.91 → scout-browser-4.91.2}/scout/parse/variant/clnsig.py

@@ -6,6 +6,17 @@ import cyvcf2
 LOG = logging.getLogger(__name__)
 
 
+def parse_clnsig_low_penetrance(sig_groups: List[str]) -> List[str]:
+    """If 'low_penetrance' is among the clnsig terms of an array, the term gets appended to the term immediately before in the array."""
+    result = []
+    for sig in sig_groups:
+        if sig == "low_penetrance" and result:
+            result[-1] += f",{sig}"
+        else:
+            result.append(sig)
+    return result
+
+
 def parse_clnsig(
     variant: cyvcf2.Variant, transcripts: Optional[dict] = None
 ) -> List[Dict[str, Union[str, int]]]:
@@ -58,6 +69,8 @@ def parse_clnsig(
             for term in significance.lstrip("_").split("/"):
                 sig_groups.append("_".join(term.split(" ")))
 
+        sig_groups: List[str] = parse_clnsig_low_penetrance(sig_groups)
+
         for sig_term in sig_groups:
             clnsig_accession = {
                 "value": sig_term,

{scout-browser-4.91 → scout-browser-4.91.2}/scout/parse/variant/genotype.py

@@ -495,7 +495,7 @@ def _parse_format_entry_trgt_mc(variant: cyvcf2.Variant, pos: int):
                 if index in pathologic_mcs:
                     pathologic_counts += int(count)
         else:
-            pathologic_counts = int(allele)
+            pathologic_counts = 0 if allele == "." else int(allele)
 
         if ref_idx is not None and idx == ref_idx:
             mc_ref = pathologic_counts

{scout-browser-4.91 → scout-browser-4.91.2}/scout/parse/variant/variant.py

@@ -92,6 +92,7 @@ def parse_variant(
 
     # cyvcf2 will set QUAL to None if '.' in vcf
     parsed_variant["quality"] = variant.QUAL
+
     parsed_variant["filters"] = get_filters(variant)
 
     # Add the dbsnp ids
@@ -235,6 +236,7 @@ def parse_variant(
 
     ###################### Add conservation ######################
     parsed_variant["conservation"] = parse_conservations(variant, parsed_transcripts)
+
     parsed_variant["callers"] = parse_callers(variant, category=category)
     set_rank_result(parsed_variant, variant, rank_results_header)
 

scout-browser-4.91.2/scout/server/blueprints/alignviewers/templates/alignviewers/utils.html

@@ -0,0 +1,5 @@
+{% macro igv_script() %}
+  <link rel="shortcut icon" href="//igv.org/web/img/favicon.ico">
+  <!-- IGV JS-->
+  <script src="https://cdn.jsdelivr.net/npm/igv@3.1.0/dist/igv.min.js" integrity="sha512-GqDTDFFltqWxc3IeSMcVcPNenhJE/OZnaMk7hkTk/shtC5bejPWstJF5AY8TsVpJWfK2HOzXYKUk95fS51Warw==" crossorigin="anonymous"></script>
+{% endmacro %}

{scout-browser-4.91 → scout-browser-4.91.2}/scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html

@@ -79,17 +79,17 @@
                 {% endif %}
                   <div class="d-flex justify-content-center">
                   {% if case.vcf_files.vcf_snv %}
-                    <form action="{{url_for('variants.variants', institute_id=institute._id, case_name=case.display_name) }}">
+                    <form action="{{url_for('variants.variants', institute_id=institute._id, case_name=case.display_name) }}" target="_blank">
                     <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="{% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %}"></input>
                     <input type="hidden" id="gene_panels" name="gene_panels" value="['']"></input>
-                    <span><button type="submit" class="btn btn-secondary btn-sm" style="float: right;" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="SNV and INDEL variants view filtered for the gene(s) {% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %} ">SNVs</button></span>
+                    <span><button type="submit" class="btn btn-secondary btn-sm" style="float: right;" data-bs-toggle="tooltip" title="SNV and INDEL variants view filtered for the gene(s) {% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %} ">SNVs</button></span>
                     </form>
                   {% endif %}
                   {% if case.vcf_files.vcf_sv %}
-                    <form action="{{url_for('variants.sv_variants', institute_id=institute._id, case_name=case.display_name) }}">
+                    <form action="{{url_for('variants.sv_variants', institute_id=institute._id, case_name=case.display_name) }}" target="_blank">
                     <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="{% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %}"></input>
                     <input type="hidden" id="gene_panels" name="gene_panels" value="['']"></input>
-                    <button type="submit" class="btn btn-secondary btn-sm" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="SV variants view filtered for the gene(s) {% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %} ">SVs</button></span>
+                    <button type="submit" class="btn btn-secondary btn-sm" data-bs-toggle="tooltip" title="SV variants view filtered for the gene(s) {% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %} ">SVs</button></span>
                   </form>
                   {% endif %}
                     </div>

{scout-browser-4.91 → scout-browser-4.91.2}/scout/server/blueprints/panels/templates/panels/panels.html

@@ -26,6 +26,9 @@
     {{ new_panel() }}
     {{ search_gene_card() }}
     {% if panel_groups %}
+      <span class="float-end me-3 mt-3">
+        <input type="checkbox" name="hideLine" checked onclick="toggleRow(this)"> Hide removed panels</input>
+      </span>
       {% for institute,panels in panel_groups %}
         {{ panel_view(institute,panels) }}
       {% endfor %}
@@ -103,7 +106,7 @@
               <select name="institute" class="form-control" required>
                 <option value="">Choose institute...</option>
                 {% for institute in institutes %}
-                  <option value="{{ institute._id }}">{{ institute.display_name }}</option>
+                  <option value="{{ institute._id }}">{{ institute.display_name }} ({{institute._id}})</option>
                 {% endfor %}
               </select>
           </div>
@@ -141,10 +144,7 @@
 {% macro panel_view(institute, panels) %}
   <div class="card panel-default w-100 mt-3 justify-content-center">
     <div class="card-title d-flex justify-content-between">
-      <span><strong>{{ institute.display_name }}</strong> - Panels</span>
-      <span>
-        <input type="checkbox" name="hideLine" checked onclick="toggleRow(this)"> Hide removed panels</input>
-      </span>
+      <span><strong>{{ institute.display_name }} ({{institute._id}})</strong> - Panels</span>
     </div>
     <div class="card-body">
         <table class="table table-striped" id="panelTable" style="table-layout: fixed;">

{scout-browser-4.91 → scout-browser-4.91.2}/scout/server/blueprints/variant/controllers.py

@@ -41,13 +41,14 @@ from scout.server.utils import (
 from .utils import (
     add_gene_info,
     associate_variant_genes_with_case_panels,
-    callers,
     clinsig_human,
     default_panels,
     end_position,
     evaluation,
     frequencies,
     frequency,
+    get_callers,
+    get_filters,
     is_affected,
     predictions,
 )
@@ -315,7 +316,10 @@ def variant(
     update_representative_gene(variant_obj, variant_genes)
 
     # Add display information about callers
-    variant_obj["callers"] = callers(variant_obj)
+    variant_obj["callers"] = get_callers(variant_obj)
+
+    # annotate filters
+    variant_obj["filters"] = get_filters(variant_obj)
 
     # Convert affection status to strings for the template
     is_affected(variant_obj, case_obj)

{scout-browser-4.91 → scout-browser-4.91.2}/scout/server/blueprints/variant/templates/variant/components.html

@@ -17,7 +17,7 @@
       <tbody>
         {% for clinsig in variant.clinsig_human %}
           <tr>
-            <td>{{ clinsig.human }}</td>
+            <td>{{ clinsig.human }} {% if clinsig.low_penetrance %}(low penetrance){% endif %}</td>
             {% if clinsig.accession %}
               <td><a href="{{ clinsig.link }}" target="_blank">{{ clinsig.accession }}</a></td>
             {% else %}

{scout-browser-4.91 → scout-browser-4.91.2}/scout/server/blueprints/variant/templates/variant/variant_details.html

@@ -97,8 +97,15 @@
       </table>
     </div>
     <div class="panel-footer">
+       {% for filter in variant.filters %} <!-- collect info from variant's filters (PASS) -->
+        <span class="badge bg-{{ filter.label_class }}" data-bs-toggle="tooltip" data-bs-placement="top" title="{{ filter.description }}">
+          {{ filter.label }}
+        </span>
+      {% endfor %}
       {% for name, caller in variant.callers %}
-        <span class="badge bg-secondary">{{ name }}: {{ caller }}</span>
+        <span class="badge {% if caller == 'Pass' %}bg-success{% elif 'Filtered' in caller %}bg-secondary{% else %}bg-black{% endif %}">
+        {{ name }}: {{ caller }}
+        </span>
       {% endfor %}
     </div>
     </div>

{scout-browser-4.91 → scout-browser-4.91.2}/scout/server/blueprints/variant/utils.py

@@ -2,7 +2,7 @@ import logging
 from typing import Dict, List, Optional, Tuple
 
 from scout.adapter import MongoAdapter
-from scout.constants import ACMG_COMPLETE_MAP, CALLERS, CLINSIG_MAP, SO_TERMS
+from scout.constants import ACMG_COMPLETE_MAP, CALLERS, CLINSIG_MAP, SO_TERMS, VARIANT_FILTERS
 from scout.server.links import add_gene_links, add_tx_links
 
 LOG = logging.getLogger(__name__)
@@ -592,14 +592,15 @@ def clinsig_human(variant_obj):
         yield clinsig_obj
 
 
-def callers(variant_obj):
+def get_callers(variant_obj: dict) -> List[Tuple]:
     """Return info about callers.
 
-    Args:
-        variant_obj(scout.models.Variant)
+    Given a scout.models.Variant compliant variant obj dict,
+    return a list of the callers that identified the variant.
 
-    Returns:
-        calls(list(str)): A list of the callers that identified the variant
+    Finds calls in the CALLERS constant for the variant category,
+    directly on the variant object, gathers them in a set of tuples
+    of caller name and status, and returns as a list of tuples.
     """
     category = variant_obj.get("category", "snv")
     calls = set()
@@ -610,6 +611,37 @@ def callers(variant_obj):
     return list(calls)
 
 
+def get_filters(variant_obj: dict) -> List[Dict[str, str]]:
+    """Return a list with richer format descriptions about filter status,
+    if available. Fall back to display the filter status in a "danger" badge
+    if it is not known from the VARIANT_FILTERS constant.
+
+    Currently, the controller may be applied repeatedly to the same variant object
+    for redecoration. Check if the filter strings have already been converted
+    to dicts before attemting to convert them.
+    """
+    variant_filters = variant_obj.get("filters", [])
+
+    filters: List[Dict[str, str]] = []
+
+    for f in variant_filters:
+        if isinstance(f, str):
+            if f.lower() in VARIANT_FILTERS:
+                filters.append(VARIANT_FILTERS[f.lower()])
+            else:
+                filters.append(
+                    {
+                        "label": f.replace("_", " ").upper(),
+                        "description": f.replace("_", " "),
+                        "label_class": "danger",
+                    }
+                )
+        elif isinstance(f, dict):
+            filters.append(f)
+
+    return filters
+
+
 def associate_variant_genes_with_case_panels(case_obj: Dict, variant_obj: Dict) -> None:
     """Add associated gene panels to each gene in variant object"""
 

{scout-browser-4.91 → scout-browser-4.91.2}/scout/server/blueprints/variants/controllers.py

@@ -27,12 +27,12 @@ from scout.constants import (
     MANUAL_RANK_OPTIONS,
     MOSAICISM_OPTIONS,
     SPIDEX_HUMAN,
-    VARIANT_FILTERS,
     VARIANTS_TARGET_FROM_CATEGORY,
 )
 from scout.server.blueprints.variant.utils import (
-    callers,
     clinsig_human,
+    get_callers,
+    get_filters,
     predictions,
     update_representative_gene,
     update_variant_case_panels,
@@ -936,14 +936,10 @@ def parse_variant(
     update_representative_gene(variant_obj, variant_genes)
 
     # Add display information about callers
-    variant_obj["callers"] = callers(variant_obj)
+    variant_obj["callers"] = get_callers(variant_obj)
 
     # annotate filters
-    variant_obj["filters"] = [
-        VARIANT_FILTERS[f]
-        for f in map(lambda x: x.lower(), variant_obj["filters"])
-        if f in VARIANT_FILTERS
-    ]
+    variant_obj["filters"] = get_filters(variant_obj)
 
     return variant_obj
 
@@ -1082,7 +1078,7 @@ def variant_export_lines_common(store: MongoAdapter, variant: dict, case_obj: di
         else variant.get("category")
     )
     variant_line.append(cat.upper() if cat else "")
-    variant_line.append("  ".join([f"{name}:{caller}" for name, caller in callers(variant)]))
+    variant_line.append("  ".join([f"{name}:{caller}" for name, caller in get_callers(variant)]))
     variant_line.append(variant["chromosome"])
     variant_line.append(position)
     variant_line.append(change)

{scout-browser-4.91 → scout-browser-4.91.2}/scout/server/blueprints/variants/templates/variants/cancer-sv-variants.html

@@ -58,8 +58,8 @@
           <tr>
             <th style="width:2%"></th>
             <th style="width:3%">Index</th>
-            <th>Type</th>
             <th style="width:9%">Callers</th>
+            <th>Type</th>
             <th style="width:5%">Chr</th>
             <th>Start</th>
             <th>End</th>
@@ -77,7 +77,7 @@
             {{ variant_row(variant) }}
           {% else %}
             <tr>
-                <td colspan="13">No matching variants</td>
+                <td colspan="14">No matching variants</td>
             </tr>
           {% endfor %}
         </tbody>
@@ -105,10 +105,10 @@
       {{ cell_rank(variant, institute, case, form, manual_rank_options) }}
     </td>
     <td>
-      {{ variant.sub_category|upper }}
+      {{ callers_cell(variant) }}
     </td>
     <td>
-      {{ callers_cell(variant) }}
+      {{ variant.sub_category|upper }}
     </td>
     <td>{{ variant.chromosome if variant.chromosome == variant.end_chrom else variant.chromosome+'-'+variant.end_chrom }}</td>
     <td class="col-2"><span style="white-space: nowrap;">{{ variant.position|human_longint|safe }}</span></td>

{scout-browser-4.91 → scout-browser-4.91.2}/scout/server/blueprints/variants/templates/variants/cancer-variants.html

@@ -62,7 +62,7 @@
               <th title="Population frequency">Pop Freq</th>
               <th title="Observed" style="width:7%">Observed</th>
               <th title="Variant type">Type</th>
-              <th title="Callers" style="width:8%">Callers</th>
+              <th title="Callers" style="width:12%">Callers</th>
               <th title="Functional consequence annotation" style="width:10%">Consequence</th>
               <th data-bs-toggle="tooltip" data-bs-placement="top" title="Tumor alt. AF. &#013; Alt. allele count | Ref. allele count">Tumor</th>
               <th data-bs-toggle="tooltip" data-bs-placement="top" title="Normal alt. AF. &#013; Alt. allele count | Ref. allele count">Normal</th>
@@ -115,7 +115,7 @@
             <td>{{ position_cell(variant) }}</td>
             <td class="text-end">{{ frequency_cell_general(variant) }}</td>
             <td>{{ observed_cell_general(variant) }}</td>
-            <td>{{ variant.sub_category }}</td>
+            <td>{{ variant.sub_category|upper }}</td>
             <td>{{ callers_cell(variant) }}</td>
             <td>{{ variant_funct_anno_cell(variant) }}</td>
             <td>{{ allele_cell(variant.tumor or {}) }}</td>

{scout-browser-4.91 → scout-browser-4.91.2}/scout/server/blueprints/variants/templates/variants/sv-variants.html

@@ -59,8 +59,8 @@ onsubmit="return validateForm()">
             <th style="width:3%"></th>
             <th>Rank</th>
             <th>Score</th>
-            <th>Type</th>
             <th>Callers</th>
+            <th>Type</th>
             <th>Chr</th>
             <th>Start</th>
             <th>End</th>
@@ -76,7 +76,7 @@ onsubmit="return validateForm()">
             {{ variant_row(variant, inherit_palette) }}
           {% else %}
             <tr>
-                <td colspan="11">No matching variants</td>
+                <td colspan="13">No matching variants</td>
             </tr>
           {% endfor %}
         </tbody>
@@ -103,14 +103,10 @@ onsubmit="return validateForm()">
       {{ cell_rank(variant, institute, case, form, manual_rank_options) }}
     </td>
     <td class="text-end">{{ variant.rank_score|int }}</td>
-    <td>
-      {{ variant.sub_category|upper }}
-    </td>
     <td>
       {{ callers_cell(variant) }}
     </td>
-    <td><span data-bs-toggle="tooltip" data-bs-html="true" title="{% for name, caller in variant.callers %}{{ name }}: {{ caller }}<br>{% endfor %}">
-      {{ variant.sub_category|upper }}</span></td>
+    <td>{{ variant.sub_category|upper }}</td>
     <td>{{ variant.chromosome if variant.chromosome == variant.end_chrom else variant.chromosome+'-'+variant.end_chrom }}</td>
     <td><span style="white-space: nowrap;">{{ variant.position|human_longint|safe }}</span></td>
 <td><span style="white-space: nowrap;">{{ 'inf' if variant.end == 100000000000 else variant.end|human_longint|safe }}</span></td>

{scout-browser-4.91 → scout-browser-4.91.2}/scout/server/blueprints/variants/templates/variants/utils.html

@@ -56,7 +56,7 @@
       </span>
     {% endfor %}
   {% for name, caller in variant.callers %} <!-- Collect info for specific callers -->
-      <span class="badge {% if caller == 'Pass' %}bg-success{% elif caller == 'Filtered' %}bg-secondary{% else %}bg-black{% endif %}" data-bs-toggle="tooltip" data-bs-html="true" title="{{caller}}">
+      <span class="badge {% if caller == 'Pass' %}bg-success{% elif 'Filtered' in caller %}bg-secondary{% else %}bg-black{% endif %}" data-bs-toggle="tooltip" data-bs-html="true" title="{{caller}}">
         {{ name }}
       </span>
   {% endfor %}

{scout-browser-4.91 → scout-browser-4.91.2/scout_browser.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.91
+Version: 4.91.2
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson