scout-browser 4.102.0__py3-none-any.whl → 4.103.1__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (59) hide show
  1. scout/adapter/mongo/case.py +26 -122
  2. scout/adapter/mongo/clinvar.py +91 -25
  3. scout/adapter/mongo/event.py +0 -47
  4. scout/adapter/mongo/variant_loader.py +7 -3
  5. scout/build/variant/variant.py +1 -0
  6. scout/commands/load/variants.py +1 -1
  7. scout/commands/update/user.py +87 -49
  8. scout/constants/__init__.py +3 -0
  9. scout/constants/clinvar.py +10 -0
  10. scout/constants/variant_tags.py +18 -0
  11. scout/demo/NIST.trgt.stranger.vcf.gz +0 -0
  12. scout/demo/NIST.trgt.stranger.vcf.gz.tbi +0 -0
  13. scout/demo/__init__.py +1 -0
  14. scout/models/clinvar.py +86 -0
  15. scout/parse/variant/coordinates.py +5 -1
  16. scout/parse/variant/gene.py +5 -9
  17. scout/parse/variant/genotype.py +66 -42
  18. scout/parse/variant/variant.py +2 -0
  19. scout/server/app.py +71 -2
  20. scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html +2 -0
  21. scout/server/blueprints/cases/controllers.py +1 -1
  22. scout/server/blueprints/cases/templates/cases/case_report.html +19 -2
  23. scout/server/blueprints/cases/templates/cases/utils.html +8 -29
  24. scout/server/blueprints/clinvar/controllers.py +233 -53
  25. scout/server/blueprints/clinvar/form.py +38 -1
  26. scout/server/blueprints/clinvar/static/form_style.css +8 -1
  27. scout/server/blueprints/clinvar/templates/clinvar/clinvar_onc_submissions.html +200 -0
  28. scout/server/blueprints/clinvar/templates/clinvar/clinvar_submissions.html +3 -2
  29. scout/server/blueprints/clinvar/templates/clinvar/components.html +198 -0
  30. scout/server/blueprints/clinvar/templates/clinvar/multistep_add_onc_variant.html +187 -0
  31. scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html +9 -348
  32. scout/server/blueprints/clinvar/templates/clinvar/scripts.html +193 -0
  33. scout/server/blueprints/clinvar/views.py +90 -13
  34. scout/server/blueprints/institutes/controllers.py +44 -5
  35. scout/server/blueprints/institutes/forms.py +1 -0
  36. scout/server/blueprints/institutes/templates/overview/gene_variants.html +15 -6
  37. scout/server/blueprints/institutes/templates/overview/institute_sidebar.html +28 -2
  38. scout/server/blueprints/institutes/templates/overview/utils.html +1 -1
  39. scout/server/blueprints/institutes/views.py +17 -4
  40. scout/server/blueprints/mme/templates/mme/mme_submissions.html +2 -2
  41. scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html +2 -2
  42. scout/server/blueprints/variant/controllers.py +1 -1
  43. scout/server/blueprints/variant/templates/variant/cancer-variant.html +2 -1
  44. scout/server/blueprints/variant/templates/variant/components.html +0 -1
  45. scout/server/blueprints/variant/templates/variant/sv-variant.html +2 -1
  46. scout/server/blueprints/variant/templates/variant/variant.html +2 -2
  47. scout/server/blueprints/variant/templates/variant/variant_details.html +33 -25
  48. scout/server/blueprints/variants/templates/variants/cancer-variants.html +5 -3
  49. scout/server/blueprints/variants/templates/variants/str-variants.html +4 -1
  50. scout/server/blueprints/variants/templates/variants/sv-variants.html +3 -3
  51. scout/server/blueprints/variants/templates/variants/utils.html +4 -0
  52. scout/server/blueprints/variants/templates/variants/variants.html +4 -4
  53. scout/server/extensions/clinvar_extension.py +2 -2
  54. scout/server/templates/layout.html +1 -1
  55. {scout_browser-4.102.0.dist-info → scout_browser-4.103.1.dist-info}/METADATA +1 -1
  56. {scout_browser-4.102.0.dist-info → scout_browser-4.103.1.dist-info}/RECORD +59 -53
  57. {scout_browser-4.102.0.dist-info → scout_browser-4.103.1.dist-info}/WHEEL +0 -0
  58. {scout_browser-4.102.0.dist-info → scout_browser-4.103.1.dist-info}/entry_points.txt +0 -0
  59. {scout_browser-4.102.0.dist-info → scout_browser-4.103.1.dist-info}/licenses/LICENSE +0 -0
@@ -1,7 +1,7 @@
1
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  {% extends "layout.html" %}
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  {% from "variants/components.html" import allele_cell, external_scripts, external_stylesheets, gene_cell, frequency_cell_general, observed_cell_general, variant_funct_anno_cell %}
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- {% from "variants/utils.html" import cancer_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, callers_cell %}
4
+ {% from "variants/utils.html" import cancer_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, callers_cell, variant_rank_score %}
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  {% from "variants/indicators.html" import pin_indicator, causative_badge, clinical_assessments_badge, comments_badge, dismissals_badge, evaluations_badge, group_assessments_badge, matching_manual_rank, other_tiered_variants, research_assessments_badge %}
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  {% block title %}
@@ -56,7 +56,7 @@
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  <th title="Gene">Gene</th>
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  <th title="Variant" style="width:12%">HGVS[c/p]</th>
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  <th title="Assessments including variant tier" style="width:8%">Assessment</th>
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- <th title="Rank scores" style="width:4%">Rank</th>
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+ <th data-bs-toggle="tooltip" title="Rank score (normalized rank score in the range 0-1)" style="width:5%">Rank</th>
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  <th title="CADD scores" style="width:4%">CADD</th>
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  <th title="Genomic coordinate" style="width:8%">Chr pos</th>
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  <th title="Population frequency">Pop Freq</th>
@@ -156,7 +156,9 @@
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  {% elif variant.rank_score > 8 %}
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  {% set label_class = 'danger' %}
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  {% endif %}
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- <div class="badge bg-{{ label_class }}" data-bs-toggle="tooltip" data-bs-placement="top" title="Rank score">{{ variant.rank_score }}</div>
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+ <div class="badge bg-{{ label_class }}" data-bs-toggle="tooltip" data-bs-placement="top" title="Rank score">
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+ {{ variant_rank_score(variant) }}
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+ </div>
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  {% endif %}
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  {% endmacro %}
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@@ -93,7 +93,10 @@
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  {% endif %}
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  <td class="str-link">{{ cell_rank(variant, institute, case, form, manual_rank_options) }}</td>
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  <td class="str-link">{{ str_locus_info(variant) }}</td>
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- <td class="text-end">{{ variant.str_display_ru or variant.str_ru or variant.reference }}</td>
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+ <td class="text-end"><span data-bs-toggle="tooltip" title="{{ variant.str_display_ru or variant.str_ru or variant.reference }}">
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+ {% if variant.str_display_ru %}{{variant.str_display_ru | truncate(12, True)}}
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+ {% elif variant.str_ru %}{{ variant.str_ru | truncate(12, True) }}
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+ {% else %}{{ variant.reference | truncate(12, True) }}{% endif %}</span></td>
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  <td class="text-end"><b><span data-bs-toggle="tooltip" title="{{ variant.alternative }}">{{ variant.str_mc }}</span></b></td>
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  <td class="text-end"><span data-bs-toggle="tooltip" title="{{ variant.reference }}">{{ variant.str_ref or "." }}</span></td>
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  <td>{{ callers_cell(variant) }}</td>
@@ -1,5 +1,5 @@
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  {% extends "layout.html" %}
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- {% from "variants/utils.html" import sv_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, callers_cell %}
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+ {% from "variants/utils.html" import sv_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, callers_cell, variant_rank_score %}
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  {% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, observed_cell_general, overlapping_cell, variant_gene_symbols_cell, variant_funct_anno_cell %}
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  {% block title %}
@@ -58,7 +58,7 @@ onsubmit="return validateForm()">
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  <tr>
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  <th style="width:3%"></th>
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  <th title="Rank position">Rank</th>
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- <th title="Rank score">Score</th>
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+ <th data-bs-toggle="tooltip" title="Rank score (normalized rank score in the range 0-1)">Score</th>
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  <th>Callers</th>
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  <th>Type</th>
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  <th title="Chromosome">Chr</th>
@@ -103,7 +103,7 @@ onsubmit="return validateForm()">
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  <td class="text-start">
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  {{ cell_rank(variant, institute, case, form, manual_rank_options) }}
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  </td>
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- <td class="text-end">{{ variant.rank_score|int }}</td>
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+ <td class="text-start">{{variant_rank_score(variant)}}</td>
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  <td>
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  {{ callers_cell(variant) }}
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  </td>
@@ -3,6 +3,10 @@
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  {% from "cases/utils.html" import pretty_link_variant %}
4
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  {% from "variants/indicators.html" import pin_indicator, causative_badge, clinical_assessments_badge, comments_badge, dismissals_badge, evaluations_badge, group_assessments_badge, matching_manual_rank, research_assessments_badge %}
5
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+ {% macro variant_rank_score(variant) %}
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+ {% if variant.rank_score %}{{ variant.rank_score|int }} {% endif %} {% if variant.norm_rank_score %} ({{variant.norm_rank_score|round(2)}}) {% endif %}
8
+ {% endmacro %}
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+
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  {% macro filter_script_main(cytobands) %}
7
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  <script type="text/javascript">
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  var startElem = document.getElementById("start");
@@ -1,5 +1,5 @@
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  {% extends "layout.html" %}
2
- {% from "variants/utils.html" import snv_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, mark_heteroplasmic_mt %}
2
+ {% from "variants/utils.html" import snv_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, mark_heteroplasmic_mt, variant_rank_score %}
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  {% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, gene_cell, observed_cell_general, overlapping_cell %}
4
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5
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  {% block title %}
@@ -55,8 +55,8 @@
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  <thead class="thead table-light">
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  <tr>
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  <th style="width:2%"></th>
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- <th style="width:12%" title="Rank position">Rank</th>
59
- <th style="width:5%" title="Rank score">Score</th>
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+ <th style="width:7%" title="Rank position">Rank</th>
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+ <th style="width:10%" data-bs-toggle="tooltip" title="Rank score (normalized rank score in the range 0-1)">Score</th>
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  <th style="width:4%" title="Chromosome">Chr.</th>
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  <th style="width:12%" title="HGNC symbols">Gene</th>
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  <th style="width:6%" title="Population Frequency">Pop Freq</th>
@@ -78,7 +78,7 @@
78
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  {% endif %}
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  <td><input type="checkbox" value="{{variant._id}}" name="dismiss" onclick="enableDismiss()"></td>
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  <td class="text-start">{{ cell_rank(variant, institute, case, form, manual_rank_options) }}</td>
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- <td class="text-end">{{ variant.rank_score|int }}</td>
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+ <td class="text-start">{{variant_rank_score(variant)}}</td>
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  <td>
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  {{ variant.chromosome }}
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  {% if variant.chromosome in ["MT","M"] %}
@@ -1,7 +1,7 @@
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  import json
2
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  import logging
3
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  from io import StringIO
4
- from typing import Optional, Tuple
4
+ from typing import Any, Optional, Tuple
5
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  import requests
7
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  from flask import flash
@@ -80,7 +80,7 @@ class ClinVarApi:
80
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  except Exception as ex:
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  return self.submit_service_url, None, ex
82
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83
- def json_submission_status(self, submission_id: str, api_key=None) -> dict:
83
+ def json_submission_status(self, submission_id: str, api_key=None) -> Any:
84
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  """Retrieve the status of a ClinVar submission using the https://submit.ncbi.nlm.nih.gov/api/v1/submissions/SUBnnnnnn/actions/ endpoint."""
85
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86
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  header: dict = self.set_header(api_key)
@@ -22,7 +22,7 @@
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  <a class="navbar-brand" href="{{ url_for('cases.index') }}">
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  <img src="{{ url_for('public.static', filename='scout-logo.png') }}" width="30" height="30" class="d-inline-block align-top text-white" alt="">Scout</a>
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  {% if config.INSTANCE_NAME %}
25
- <span class="badge bg-light text-dark">
25
+ <span class="navbar-text badge bg-light text-dark">
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  {{ config.INSTANCE_NAME }}
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  </span>
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  {% endif %}
@@ -1,6 +1,6 @@
1
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  Metadata-Version: 2.4
2
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  Name: scout-browser
3
- Version: 4.102.0
3
+ Version: 4.103.1
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  Summary: Clinical DNA variant visualizer and browser
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  Project-URL: Repository, https://github.com/Clinical-Genomics/scout
6
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  Project-URL: Changelog, https://github.com/Clinical-Genomics/scout/blob/main/CHANGELOG.md
@@ -4,14 +4,14 @@ scout/adapter/client.py,sha256=IuajRsEwTG41ZP14X09Q1Cj94zIgmIvUtlXfcAFn0EA,1513
4
4
  scout/adapter/mongo/__init__.py,sha256=NdHYCUXWUAuX5cUS3-6HCws2hW9uoGep8i0SC-oJd3k,31
5
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  scout/adapter/mongo/acmg.py,sha256=v2Zuw-6APVmcnBnNXa18WJEu2vj5GUhZNiKMkruJsBI,4170
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  scout/adapter/mongo/base.py,sha256=iIa2AjGNztKHcZzolY0T6r7Oh0guj6R1putztp4OTNY,4427
7
- scout/adapter/mongo/case.py,sha256=Cqb_uWbW5gnAoOMoJVK9LYeCrJEE-M3fgI97-3t6gbc,66613
7
+ scout/adapter/mongo/case.py,sha256=udbugVMaza3qpIdQ4C9NpDkBEg1WN0MVakdWNow5cwA,63093
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  scout/adapter/mongo/case_events.py,sha256=slHR4XJF9vRuEbuInJKMMAImLF8m7tHWVfGP42fbXr0,26859
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  scout/adapter/mongo/case_group.py,sha256=tG8DuO0rNYepV4k0yCGPqssODErc0HMsAypg3mfhcV0,1575
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  scout/adapter/mongo/ccv.py,sha256=VIz-Yqzm-1UVPDKvZkBllO4BOKXzvKCXcQUjTtZCHTI,4165
11
- scout/adapter/mongo/clinvar.py,sha256=qaUrpO_eQfy2ZAAaNKOtLKxCgrMatEVhqHbJ__kXTI4,19462
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+ scout/adapter/mongo/clinvar.py,sha256=U48oocMB40-JZfajJ3PBmtS5ZUFeMfnhokB4o3iHNTg,22712
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  scout/adapter/mongo/cytoband.py,sha256=2NoIAoQ7RPqcipiSymD2O9qH8lXscP3T5ejquOrD7uQ,2622
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  scout/adapter/mongo/disease_terms.py,sha256=4qcQRLuP5xn_RkB2RlNtwCrONmDuWwdlngZrj87BUEo,5637
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- scout/adapter/mongo/event.py,sha256=xC6VdfZUU8tIPKZrCklD-zX3wgfZD09ze5wrpyLbkIA,20245
14
+ scout/adapter/mongo/event.py,sha256=Xoq009ht7sRXkxglvO74n-LVa9gpA96j4yXiEmH6VnI,18684
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  scout/adapter/mongo/filter.py,sha256=rIdjiDJCrNDeTNgssKm7n1HTxne72jvlX2I3FQjQGo8,9687
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  scout/adapter/mongo/hgnc.py,sha256=S7CFw1DAP-jHGgybw-3H2Dozn5s1rYxnJMHnl8GArKU,16680
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  scout/adapter/mongo/hpo.py,sha256=ps2Pix3sGeea7DenboZVP5j7Vh9WAgX3-sgpbAj0Eck,6871
@@ -28,7 +28,7 @@ scout/adapter/mongo/transcript.py,sha256=3U1qtyxZ1DnrzdBJm_emJXISMYFKJuX_zAKynUt
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  scout/adapter/mongo/user.py,sha256=QoQnRWqi_dV3ZwGzBonEU6Ap9TgMDf2x_C5UIqG0pa0,2569
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  scout/adapter/mongo/variant.py,sha256=IMZcRr43b3XsDqi9kpymobAj_CPVQkN_rxLMfxQ75LI,36267
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  scout/adapter/mongo/variant_events.py,sha256=yNnMM58P1LbYFw73rWzti6l2zWa_G93ozUTbVkcz4_I,33475
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- scout/adapter/mongo/variant_loader.py,sha256=u7XNy3-RjMg80c4iUV2FLfIjfCm286uC0HzHFeiJmh4,28674
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+ scout/adapter/mongo/variant_loader.py,sha256=GPvqfcL5hmd4fUKbTshwKZHvT_Wx4f_vrJ_lEi4Jjk0,28732
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  scout/build/__init__.py,sha256=GUWEaXTpwsJil_KtrXBQJpZIwCQFSgo8NlK49R9IkA8,521
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  scout/build/acmg.py,sha256=M21MrrP_dtEyOuu6t-jBDdaqYcHPMLcwJlt9fHG2ycE,1523
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  scout/build/case.py,sha256=LtYx6zQcCoGCss48qf7uluzTlXVH0Pl-WhqYzkbIcZ8,11510
@@ -50,7 +50,7 @@ scout/build/variant/compound.py,sha256=tYikQ4PmgAH1_yrE9uYaUX4_EoAs_XEiT8JWAjrZu
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  scout/build/variant/gene.py,sha256=Fj_ouJtNAZOvxYVo9oVXaYJE5_zx-mJqL-uOARD4ku8,3857
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  scout/build/variant/genotype.py,sha256=QDTZWFB8ix9Zd1m9UPWgT008i6rC7gT-uFzRr9GniDU,1009
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  scout/build/variant/transcript.py,sha256=hf_led1kdT3hVEwtHdORhBSk6a6o_zEDJ0z4ZF8IlFA,1205
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- scout/build/variant/variant.py,sha256=KHBf5dZt3i0tz8pN4Bujp7edI754cnb5jN4wcsTesVc,18740
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+ scout/build/variant/variant.py,sha256=Iw9vxWSfyGgD3XtknqAVAmAc87NxpbiHKZvCJS-P8v4,18811
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  scout/commands/__init__.py,sha256=VrenBj1daCAnIsBZtvdbv1SuxmODT_TTY8YcxWItrXE,22
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  scout/commands/base.py,sha256=WmUko96zsPbC3cUIezy0CAOOGKBFU-BoW-BPAhLORCE,4610
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  scout/commands/convert.py,sha256=T5dkFjRKSTf7dBS9uKIW4wEmdL13vKzKTLRy4nvf6Vg,1090
@@ -93,7 +93,7 @@ scout/commands/load/region.py,sha256=psICLlMf5WBdSCgXsJZUsM8fICsTJB3Q6U6dB5S6w_8
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  scout/commands/load/report.py,sha256=DrnyOJcLbOUUJHzI3jwlj955zYohvjuTeeoeUS_ZU8Q,3564
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  scout/commands/load/research.py,sha256=t5a6kVVPX3aZtDx20VNNXhkAGTB_gCln5Ejjy_JjYGE,4418
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  scout/commands/load/user.py,sha256=eDHt_byU3DVhI9D-3GwEW_VpQbIF6bPEORAieCTcdUc,1412
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- scout/commands/load/variants.py,sha256=XnF5p_ZAltPgOnmGYtS4tuvJcVEZf7L6K9p6IdYfuEQ,9972
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+ scout/commands/load/variants.py,sha256=3hloGZ51MlAc-1OU9gMsKr4KQbwcR5__5fQRVPFCPpk,9957
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  scout/commands/setup/__init__.py,sha256=uiuizwirbfLqp93K4__b982obk1stkzwpvXHi51OAbE,31
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  scout/commands/setup/setup_scout.py,sha256=txS4tRwk1FMlS_qkyJl0XaZU0rFivqVCMqMi7iZtw78,9254
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  scout/commands/update/__init__.py,sha256=yKNjRTVFsSTko8T7znfMqSI_HsGPN2-z1c0twkwO5uE,25
@@ -109,7 +109,7 @@ scout/commands/update/omim.py,sha256=s39qterBGhtBfW7Uc-IJabni93PIhT8shqVbkmQBb9k
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  scout/commands/update/panel.py,sha256=990shZ15k5pwHUkd767o8oQ5iqVIpgRA7N_9yv1_eqc,2912
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  scout/commands/update/panelapp.py,sha256=lUDuN8iLPwUFFG_iY35L5gDEjrgsE22Eo_xB1Djj1_4,1922
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  scout/commands/update/phenotype_groups.py,sha256=Ll0COlEckn1Z7VAJbFbG2EZ5FKFVEcff0sWiUsx-D-g,1980
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- scout/commands/update/user.py,sha256=s5s7nh9UABBO9P6L11_j5tsi4iPxzieHw40yDhc4PWM,2497
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+ scout/commands/update/user.py,sha256=WGilEwo9aVv3_z7ZBJBSoeY7sGhPU7UHcp3rERTcJgk,3681
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  scout/commands/view/__init__.py,sha256=ZtRW7UBNf1rPnlCslBVcmjafOPg9WTPpn4xxlAA0wMo,23
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  scout/commands/view/aliases.py,sha256=M0hTBHk_cyW-BG0cNz5T3q20waYP4ktTfTCzCtkTUs0,1995
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  scout/commands/view/base.py,sha256=Lz2cB7yTPjHXLgDu3aumHm6d4ozAKEA5V5ff1NAT4wA,1000
@@ -125,11 +125,11 @@ scout/commands/view/intervals.py,sha256=8Pofxy0DwL2Euh3SdnTLLWsU6DjLNOwIGdxeCS83
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- scout/constants/__init__.py,sha256=nUd4T3RwBSNcxiU8rXZDOd8nPRl2gqWILY-C0SflnzE,5969
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+ scout/constants/__init__.py,sha256=yJga2nPS9l0oC89jwE2FXt7zmMC8Fr8AW1rIgwfvaDU,6067
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- scout/constants/clinvar.py,sha256=nr7KhwMIO_7taNQokRJlpgZfenMlKsdPIMpdOx3TwKY,5594
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+ scout/constants/clinvar.py,sha256=MGGwEaKIsvrG6EU9CYIeFmOuxQnQ-c6haoE9ePUL2z0,5946
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@@ -141,7 +141,7 @@ scout/constants/panels.py,sha256=1N2Ys94IxoEWxySTJDW-rFJ55vtCkqnn6bRWjkw61J4,876
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- scout/constants/variant_tags.py,sha256=NnpcJGRDycq3PIrDQsd57ynJ8NzmJETICBVjzGKZlSg,17907
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+ scout/constants/variant_tags.py,sha256=Ku5pPLcnFwmjViScTBR8TSUP9HAfrKAkISZ4xfL2mNg,18821
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@@ -189,7 +189,9 @@ scout/demo/ADM1059A2.d4,sha256=M4ubAb6oVkr8dOkvkROkTr76nACfE4eSWHiUKN5FRLg,61119
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- scout/demo/__init__.py,sha256=ggXVz3_6ZUAzIZtuaK8kz3C6BuxSfaQ56PAzinJcYoI,2061
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+ scout/demo/NIST.trgt.stranger.vcf.gz,sha256=st-MDy7qyBbCEulaLcOt04ZpTTnEQBQHH7BpWDjuZhE,9392
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+ scout/demo/NIST.trgt.stranger.vcf.gz.tbi,sha256=SUfn5hujVKZHznh2EbulqzKEfSFDC7pjx8J9PitjXOQ,3771
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+ scout/demo/__init__.py,sha256=oqrUngZAPCUFWV1OWeFbEewatgFd91HLKjoWPoqcGHM,2137
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  scout/demo/cancer.load_config.yaml,sha256=MWoxppBQo4VHCTj-CzKClHSRWmTJyH1KgDy2-_m8RV4,1385
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@@ -388,7 +390,7 @@ scout/log/log.py,sha256=EPtd6Z1HMSvmuDHdElLUcLhPsz36LNQSX09Lg3m1jCY,1549
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- scout/models/clinvar.py,sha256=fTmQYV3yRxQn1JBOwKnovYmkl19H14HKRE2zY9JA93U,3102
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+ scout/models/clinvar.py,sha256=HHnTHnJdO054HDNlTQv6EHdzjsnwM0c_Aq6ZznoMo8M,5320
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@@ -430,24 +432,24 @@ scout/parse/variant/callers.py,sha256=eA5o4Ov_v5ds__4xpif1ttj5yk2nK4GXwhYSWL4NTD
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- scout/parse/variant/coordinates.py,sha256=CU-EyD8NVgTbyIdmYDO3k-zVaMN1EDONjorDwyUSnXU,4742
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+ scout/parse/variant/coordinates.py,sha256=j3pJzH3sZguD7d3J908Jon1NuXBk4FIyL2pjTW57Tdo,4896
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- scout/parse/variant/gene.py,sha256=30SR2ck12HQW87LlRfchdgPVzOxb74aIXC2WzPL2BPk,4688
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- scout/parse/variant/genotype.py,sha256=mGgTFC6DrSEzYyAbbIfdUcnxUOxdfnpNAFzKazC4pJ0,16452
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+ scout/parse/variant/gene.py,sha256=MMLvOoQYx-e3mi9vcZv0pqzWQ0bsF7kywmXav_4xwzg,4529
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+ scout/parse/variant/genotype.py,sha256=NRUMohsWa2ADh45p7R8iDK5VYTBTrQCzq5C3OrV95D4,17471
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- scout/parse/variant/variant.py,sha256=3K7OQ2OFvAbE7s5rD8178oUvHJJ2qIcn2NeBQ8o_i60,24768
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+ scout/parse/variant/variant.py,sha256=5sIEZifYf82sDIk9d0tbBWX-K4vRXs17rxYXsCGZCpk,24883
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  scout/resources/__init__.py,sha256=i9UVG651subgmOZ-Gm-JKPsXBqr5-50QUDfSpbwmwIw,443
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  scout/resources/cytoBand_hg19.txt.gz,sha256=pheUD5b9NlVuvwwnbKwDc2FG80Yg70gvPxVXP-Sqd3k,6147
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  scout/resources/cytoBand_hg38.txt.gz,sha256=sqSVmvPlktQ-0hTiTapJM-5UgyV6xDoYZuTF0kPuETs,6105
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  scout/server/__init__.py,sha256=iwhKnzeBJLKxpRVjvzwiRE63_zNpIBfaKLITauVph-0,24
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- scout/server/app.py,sha256=0Vmhzl7BviwbFA6ZsnXDM-E_KM6kEEWraCUxm8qMvc4,12011
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+ scout/server/app.py,sha256=NB3WXI2Xa8Wdfnonkoxb0mWeEV9gYOJhqvYc_h4ajTw,14633
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  scout/server/auto.py,sha256=8B6GwfOaUChkTLuLgYQDFMWlxGuHkEegF1argH2G2Ik,401
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  scout/server/links.py,sha256=aFCvrtXrc1gnhNhnifapVdUZOZKEpBD2zSxWXdvQLEk,28154
@@ -458,12 +460,12 @@ scout/server/blueprints/alignviewers/controllers.py,sha256=s8fvqOewsR9bSf-tbZFGe
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  scout/server/blueprints/alignviewers/partial.py,sha256=9hpI00yhvZZCcPVUHlVDp488r1j7vYU5YDXYA6OkWQM,2005
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  scout/server/blueprints/alignviewers/views.py,sha256=Qa9VOPbqh2MC-L_x1Yp6n8hfr6mIm9EPIUdN_0itJRU,5092
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  scout/server/blueprints/alignviewers/templates/alignviewers/igv_sashimi_viewer.html,sha256=37ArJCraTajqWlCvyQYVfSvWCg94pRDIMvf2Y7Oe_j4,5545
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- scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html,sha256=1DUcfgoFMJDBYHuZ5IwNvbs0fHSDjWJdmNS_GxIbSjE,10891
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+ scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html,sha256=rm_qcJaySQ3-Ux8Qr5JXlzWGFPAnx24fqa-XMpdcCnI,10988
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- scout/server/blueprints/cases/controllers.py,sha256=O3Emj0WOdVbsZBuGNbnNIow7qudYHBob3ATcNhOGniY,57728
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+ scout/server/blueprints/cases/controllers.py,sha256=iXL_o8LsBYP3efBBt3_vmNPKzBfWg6Nouimz4QMBMrc,57728
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  scout/server/blueprints/cases/static/case_styles.css,sha256=2Pgc8pFf9DR5HM1sTdAjaRWhjL-bK5bsQnLpH54HZak,541
@@ -471,7 +473,7 @@ scout/server/blueprints/cases/static/edit_pedigree.js,sha256=ntC5fie7SsOYJau8qkk
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  scout/server/blueprints/cases/static/madeline.js,sha256=KHxKMBVlYVJODNu5QkY9hhsGkDJNoaCoCZZ0DRu0YN0,1175
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  scout/server/blueprints/cases/templates/cases/case_bionano.html,sha256=PLoRv7hDJcHwxhi-0hC9fQSZc7V_aUYHBhhQqcn_2G8,5946
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- scout/server/blueprints/cases/templates/cases/case_report.html,sha256=9JAa3P1yWxOel71QnJYjJyaBKF6Odi42kbZEdofzOe4,65118
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+ scout/server/blueprints/cases/templates/cases/case_report.html,sha256=1_4QUmBUv4HoMv-1zbY6JI1MEN2Or9c9Zqu-sQDzzgo,65815
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  scout/server/blueprints/cases/templates/cases/case_sma.html,sha256=99rmRyDXFXjooB52TI5_ebJKv1ZAJbVXEw4deHfSVMA,7285
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  scout/server/blueprints/cases/templates/cases/chanjo2_form.html,sha256=WwdEfVtreTOruPrUJbasGE2Zmt3FiCSHwNEcJVRmefQ,2203
@@ -483,15 +485,19 @@ scout/server/blueprints/cases/templates/cases/individuals_table.html,sha256=KMWl
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  scout/server/blueprints/cases/templates/cases/phenotype.html,sha256=C0PEB2VKbQ7i3cOtAJn4NZSzRGCHolI2VbWtOjWwk64,16416
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- scout/server/blueprints/cases/templates/cases/utils.html,sha256=V99UYEXJtFOuQyLnEXjEEPpqBXediJtc7FvHoNTyh8A,36682
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+ scout/server/blueprints/cases/templates/cases/utils.html,sha256=Dx-TWaK_B3Ksz8V3DkS4nX6tUUUC7R3LFPekOniFPzk,35487
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- scout/server/blueprints/clinvar/controllers.py,sha256=9KpswGFEaejwMevgcG2D8IRqr6GHRMSAt28ZhkPbE6s,25015
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- scout/server/blueprints/clinvar/form.py,sha256=2h42YJzaOtsdEglxqt7F1i2ncjSU_IHNt-m4QOJytK4,5148
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- scout/server/blueprints/clinvar/views.py,sha256=p4R31xEBqvyw9bbwrB_rRe4UqIDc3HPTvhiVhZ1Z_lA,5760
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- scout/server/blueprints/clinvar/static/form_style.css,sha256=Tro2w0Su9st2ZRpt8PjF7qXYet-0n6Eyol4oh94JafU,4073
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+ scout/server/blueprints/clinvar/controllers.py,sha256=hTpGRdwmlDmd3xa-T4cTpfkGFGHrDDAEXcgToVe0juc,32211
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+ scout/server/blueprints/clinvar/form.py,sha256=pv9p3do4Z_DIdnIyqwEM8ckCmuHbnYPORqW-ezsyREs,6440
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+ scout/server/blueprints/clinvar/views.py,sha256=DfY3ua_sBvpsNvEySQuWNIv5VpICiSqIomAw_fa6A6c,8927
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+ scout/server/blueprints/clinvar/static/form_style.css,sha256=b-cDwPKMOIkivOZi3XiLP9xMwPKYCPKaUKB1QdvpEoY,4143
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- scout/server/blueprints/clinvar/templates/clinvar/clinvar_submissions.html,sha256=XvS6WR7xPy3KNB9q9sWzAsXf2QAjkxGeMaJlx6BkeVE,18694
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- scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html,sha256=ilDxkFUUDMy6Qzcby2BKJ21zmpI1HYI1ZC4HmrGYLpk,32953
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+ scout/server/blueprints/clinvar/templates/clinvar/clinvar_onc_submissions.html,sha256=48CzsbN0OZKQCAkxhWX2F7hmOgL-44rl911f99qrRdQ,10474
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+ scout/server/blueprints/clinvar/templates/clinvar/clinvar_submissions.html,sha256=ak5QSOXvi_Xt8JnmjIi1pDzU_NXKJiJkbqTVmw_79lI,18773
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+ scout/server/blueprints/clinvar/templates/clinvar/components.html,sha256=oO8UBUO6JG5uGad7ejII4mkUaI9BiGi1BQGpG-ETva0,9269
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+ scout/server/blueprints/clinvar/templates/clinvar/multistep_add_onc_variant.html,sha256=Sx7mZkxEIpebnGYeZpnpc2fGjKzZ1F-Nid3qJA4FXFM,9809
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+ scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html,sha256=tejiVcPVWNgGMKcOcAQaW9MklzslmR0YT9OMQGhDtOU,17386
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+ scout/server/blueprints/clinvar/templates/clinvar/scripts.html,sha256=cVApkmHrAGpkgOJzcXB-Ot7T7clhL_F8N3JxrLKJ6uo,6443
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  scout/server/blueprints/dashboard/forms.py,sha256=vbdkujKZxVjiZw2inNhysN3yYMPCdMPbqvKV88DamwI,501
@@ -511,9 +517,9 @@ scout/server/blueprints/genes/templates/genes/gene.html,sha256=a--c-IjzNKN_JW7z9
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  scout/server/blueprints/institutes/__init__.py,sha256=kGSyYrBC1QaEQBDdoMkMLfaowV7roaV5DowICi_0RSQ,65
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- scout/server/blueprints/institutes/controllers.py,sha256=TbKTIHkIsgtRJKyW1Cjya2BbUYT3wjZgfGUS4ziM6Gg,35543
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- scout/server/blueprints/institutes/forms.py,sha256=uKyl1bfAFYB65P0DHMihBWhE9bvxNixAIkznuelpIBo,6810
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- scout/server/blueprints/institutes/views.py,sha256=PSpf82kW0EKZc24CPhBhuE-wXXGyIz-R6IJu7IM0IrM,9052
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+ scout/server/blueprints/institutes/controllers.py,sha256=nYAkZ2SRBQsXYm-rfMkfyxBTWGSrpsgnvGdZ9Qqsqk0,37115
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+ scout/server/blueprints/institutes/forms.py,sha256=1xz_p51YIlWv-VhkCD3WS0K1z1S1oPYuWNaUNAQOchk,6858
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+ scout/server/blueprints/institutes/views.py,sha256=LG-uTAEUxbkHvvk0YDeDak2v366lAhmFjsyGYbZGI48,9354
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@@ -521,12 +527,12 @@ scout/server/blueprints/institutes/static/variants_list_scripts.js,sha256=R4rqoC
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- scout/server/blueprints/institutes/templates/overview/gene_variants.html,sha256=EyhBZEdMZQBaJWR_FDeabuWXRSd4Xcqh0teaxVyNvAE,8442
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+ scout/server/blueprints/institutes/templates/overview/gene_variants.html,sha256=2D9KUxcB5Ez0iJjNDtzbEP01g4iYNKG9MkaMWsdBlak,8853
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- scout/server/blueprints/institutes/templates/overview/institute_sidebar.html,sha256=_v2a-GAB6xEbLdxj5JlH3llM2HS7MFFV2zd89QLkDWU,4740
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+ scout/server/blueprints/institutes/templates/overview/institute_sidebar.html,sha256=cBr3xfns7BO4Gn-YGyDc-wG3hHB-mC-lfbMYu7nFcxQ,5800
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- scout/server/blueprints/institutes/templates/overview/utils.html,sha256=zkoqVNdBaeUtGFQfCNb7Vo3GlOypjg42XS0GvHlih7o,34297
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+ scout/server/blueprints/institutes/templates/overview/utils.html,sha256=H3W65bXkBMpsB2EIc2zdm9e-NGsE10XvJh87rrh20Ro,34346
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@@ -549,11 +555,11 @@ scout/server/blueprints/managed_variants/templates/managed_variants/managed_vari
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- scout/server/blueprints/mme/templates/mme/mme_submissions.html,sha256=OUO_3b0qEat82g8CWX9sy6-pyWdTDtIWs-y2fnhM1Io,4681
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+ scout/server/blueprints/mme/templates/mme/mme_submissions.html,sha256=VjahYVVpvyYKStbRmnvlGoHBG4k7W04hYytgTrITsCA,4707
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+ scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html,sha256=tf46LDyQbxM8vshTs-MkZiMc0ClV-9LDUVRAtxNv5o4,14005
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@@ -611,24 +617,24 @@ scout/server/blueprints/public/static/ideograms/chromosome-X.png,sha256=Dj7npcW_
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+ scout/server/blueprints/variant/templates/variant/cancer-variant.html,sha256=moeQ2I-gIGG1ecG-7Aa2f9EdA_uLYu-pUkEwLfpr0O4,14876
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+ scout/server/blueprints/variant/templates/variant/components.html,sha256=qqzxAJGmwP7DFdu91j2LSAXiBSuIWRmdB7Q6BiHWabE,28497
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- scout/server/blueprints/variant/templates/variant/sv-variant.html,sha256=Jqhp0Co3AsZO1pEM7Iw2Cwa-nYs3KM_TBGxZP9KgfL4,16825
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+ scout/server/blueprints/variant/templates/variant/sv-variant.html,sha256=IDg44nyjtdlzJ5S3-_Ba8lyGKYwszz-0mYhy8MsQ-mE,16891
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- scout/server/blueprints/variant/templates/variant/variant.html,sha256=KbB-MjLehWeD4mEKevx0R6g6PJP0BjJ_cPLBlqOXmPc,20714
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- scout/server/blueprints/variant/templates/variant/variant_details.html,sha256=RkqkHkhH1ireRBKYA0GwoTwowTxHwJgehYckveOw6-I,21039
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+ scout/server/blueprints/variant/templates/variant/variant.html,sha256=Pn4OSSgXjbsLXUbEKOqKKhyNsny4Ay-hoBFY1xDZ-dw,20741
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+ scout/server/blueprints/variant/templates/variant/variant_details.html,sha256=Bs59vFzJMav7D65aNLOQZ5985t0ZK49uyE1go_h5MdQ,21960
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@@ -636,21 +642,21 @@ scout/server/blueprints/variants/utils.py,sha256=ifFBoyigx0A5KPE4iz9NSpyuUeF1bEl
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- scout/server/blueprints/variants/templates/variants/cancer-variants.html,sha256=iEL4InO43JGwZP0QDC5VA-4LcZtIadm8d1FFI8mFb-M,9689
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+ scout/server/blueprints/variants/templates/variants/cancer-variants.html,sha256=Czn1sp5hCsRZ_UoVuqU-lROeD4Ph1rhzAeG7sAA-ltM,9795
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- scout/server/blueprints/variants/templates/variants/str-variants.html,sha256=n424D8xV76bCKDSFzzIsWfFAoU2dAYE-PPZyTtQeMdM,10924
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- scout/server/blueprints/variants/templates/variants/utils.html,sha256=g6nvYsYwhlXP7ubT1mEX0zU9cAXIZ8KJWHvTFzMCxNI,52919
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- scout/server/blueprints/variants/templates/variants/variants.html,sha256=oqJdyiIVwhZKnOGDfx07dPlRduIUvN5r0JmmK4hYExQ,8450
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+ scout/server/blueprints/variants/templates/variants/str-variants.html,sha256=Hkn6gO0Cjc8APkdNAMfya87yIecqtEzeftIP6WjDP2g,11210
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+ scout/server/blueprints/variants/templates/variants/sv-variants.html,sha256=7SZEkk4wjNOmgLdBcRKnNC8jdiLgPDsKey5CsQR1x8A,6794
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+ scout/server/blueprints/variants/templates/variants/utils.html,sha256=tAggwsNLqPp2YW8XH5Q7HkBTiGbYB_NmptmbYIfE4xs,53129
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+ scout/server/blueprints/variants/templates/variants/variants.html,sha256=eRbO7vnbH2Ainv7Lq9VFnLaijLwFSTX_XiHDyhtDEYo,8541
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+ scout/server/extensions/clinvar_extension.py,sha256=c-SXg2c6y5Plq5XM8AC7SJx96_I3TxfoxEwMKhEQnSw,6336
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@@ -665,7 +671,7 @@ scout/server/static/favicon.ico,sha256=8aC2QonalUW-D62draMeiII4sZYQSp9BLGQnj-wRl
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+ scout/server/templates/layout.html,sha256=qsi-Zx56xYC4VU2TpfrgSW2sinZHcOaQcYRrALA7Qrs,5127
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@@ -689,8 +695,8 @@ scout/utils/link.py,sha256=HpQvwu0hmuCrs7TcAExLmOzEGr3glWuu8iaW0ao5pEA,9011
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- scout_browser-4.102.0.dist-info/METADATA,sha256=Dzeha9Ho1ykmvcAzIodqT_hxJeNAqr333lP4-g3iSzY,15527
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- scout_browser-4.102.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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- scout_browser-4.102.0.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
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- scout_browser-4.102.0.dist-info/licenses/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
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- scout_browser-4.102.0.dist-info/RECORD,,
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+ scout_browser-4.103.1.dist-info/METADATA,sha256=2M-_b7t4sUVFinaL396kgjRk5dpX7cWsnTJieF8vYWU,15527
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+ scout_browser-4.103.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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+ scout_browser-4.103.1.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
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+ scout_browser-4.103.1.dist-info/licenses/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
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+ scout_browser-4.103.1.dist-info/RECORD,,