scout-browser 4.102.0__py3-none-any.whl → 4.103.0__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.
- scout/adapter/mongo/case.py +26 -122
- scout/adapter/mongo/clinvar.py +91 -25
- scout/adapter/mongo/event.py +0 -47
- scout/adapter/mongo/variant_loader.py +7 -3
- scout/build/variant/variant.py +1 -0
- scout/commands/load/variants.py +1 -1
- scout/commands/update/user.py +87 -49
- scout/constants/__init__.py +3 -0
- scout/constants/clinvar.py +10 -0
- scout/constants/variant_tags.py +18 -0
- scout/demo/NIST.trgt.stranger.vcf.gz +0 -0
- scout/demo/NIST.trgt.stranger.vcf.gz.tbi +0 -0
- scout/demo/__init__.py +1 -0
- scout/models/clinvar.py +86 -0
- scout/parse/variant/coordinates.py +5 -1
- scout/parse/variant/gene.py +5 -9
- scout/parse/variant/genotype.py +66 -42
- scout/parse/variant/variant.py +2 -0
- scout/server/app.py +71 -2
- scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html +2 -0
- scout/server/blueprints/cases/controllers.py +1 -1
- scout/server/blueprints/cases/templates/cases/case_report.html +19 -2
- scout/server/blueprints/cases/templates/cases/utils.html +8 -29
- scout/server/blueprints/clinvar/controllers.py +233 -53
- scout/server/blueprints/clinvar/form.py +38 -1
- scout/server/blueprints/clinvar/static/form_style.css +8 -1
- scout/server/blueprints/clinvar/templates/clinvar/clinvar_onc_submissions.html +200 -0
- scout/server/blueprints/clinvar/templates/clinvar/clinvar_submissions.html +3 -2
- scout/server/blueprints/clinvar/templates/clinvar/components.html +198 -0
- scout/server/blueprints/clinvar/templates/clinvar/multistep_add_onc_variant.html +187 -0
- scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html +9 -348
- scout/server/blueprints/clinvar/templates/clinvar/scripts.html +193 -0
- scout/server/blueprints/clinvar/views.py +90 -13
- scout/server/blueprints/institutes/controllers.py +44 -5
- scout/server/blueprints/institutes/forms.py +1 -0
- scout/server/blueprints/institutes/templates/overview/gene_variants.html +15 -6
- scout/server/blueprints/institutes/templates/overview/institute_sidebar.html +28 -2
- scout/server/blueprints/institutes/templates/overview/utils.html +1 -1
- scout/server/blueprints/institutes/views.py +17 -4
- scout/server/blueprints/mme/templates/mme/mme_submissions.html +2 -2
- scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html +2 -2
- scout/server/blueprints/variant/controllers.py +1 -1
- scout/server/blueprints/variant/templates/variant/cancer-variant.html +2 -1
- scout/server/blueprints/variant/templates/variant/components.html +0 -1
- scout/server/blueprints/variant/templates/variant/sv-variant.html +2 -1
- scout/server/blueprints/variant/templates/variant/variant.html +2 -2
- scout/server/blueprints/variant/templates/variant/variant_details.html +32 -24
- scout/server/blueprints/variants/templates/variants/cancer-variants.html +5 -3
- scout/server/blueprints/variants/templates/variants/str-variants.html +4 -1
- scout/server/blueprints/variants/templates/variants/sv-variants.html +3 -3
- scout/server/blueprints/variants/templates/variants/utils.html +4 -0
- scout/server/blueprints/variants/templates/variants/variants.html +4 -4
- scout/server/extensions/clinvar_extension.py +2 -2
- scout/server/templates/layout.html +1 -1
- {scout_browser-4.102.0.dist-info → scout_browser-4.103.0.dist-info}/METADATA +1 -1
- {scout_browser-4.102.0.dist-info → scout_browser-4.103.0.dist-info}/RECORD +59 -53
- {scout_browser-4.102.0.dist-info → scout_browser-4.103.0.dist-info}/WHEEL +0 -0
- {scout_browser-4.102.0.dist-info → scout_browser-4.103.0.dist-info}/entry_points.txt +0 -0
- {scout_browser-4.102.0.dist-info → scout_browser-4.103.0.dist-info}/licenses/LICENSE +0 -0
@@ -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"><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>
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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 %}
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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>
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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-
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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>
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{% from "cases/utils.html" import pretty_link_variant %}
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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 %}
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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 %}
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{% endmacro %}
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{% macro filter_script_main(cytobands) %}
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<script type="text/javascript">
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var startElem = document.getElementById("start");
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{% extends "layout.html" %}
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{% 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 %}
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{% 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 %}
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{% block title %}
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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:
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<th style="width:
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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>
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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-
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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"] %}
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import json
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import logging
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from io import StringIO
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from typing import Optional, Tuple
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from typing import Any, Optional, Tuple
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import requests
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from flask import flash
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except Exception as ex:
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return self.submit_service_url, None, ex
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def json_submission_status(self, submission_id: str, api_key=None) ->
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def json_submission_status(self, submission_id: str, api_key=None) -> Any:
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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."""
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header: dict = self.set_header(api_key)
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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 %}
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<span class="badge bg-light text-dark">
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<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 %}
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Metadata-Version: 2.4
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Name: scout-browser
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Version: 4.
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Version: 4.103.0
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Summary: Clinical DNA variant visualizer and browser
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Project-URL: Repository, https://github.com/Clinical-Genomics/scout
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Project-URL: Changelog, https://github.com/Clinical-Genomics/scout/blob/main/CHANGELOG.md
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@@ -4,14 +4,14 @@ scout/adapter/client.py,sha256=IuajRsEwTG41ZP14X09Q1Cj94zIgmIvUtlXfcAFn0EA,1513
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scout/adapter/mongo/__init__.py,sha256=NdHYCUXWUAuX5cUS3-6HCws2hW9uoGep8i0SC-oJd3k,31
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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
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scout/adapter/mongo/case.py,sha256=
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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
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scout/adapter/mongo/clinvar.py,sha256=
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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=
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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
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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=
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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
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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=
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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
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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=
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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
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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=
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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
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scout/commands/view/panels.py,sha256=a0fQcP9-SDPuRYV7aEgIGUCYaMN6V47h6finpcdoomU,1098
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scout/commands/view/transcripts.py,sha256=59WyNNp7zHPJIz9QgzrkoeKaSXTtuLli0VuL8IidEmY,1277
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scout/commands/view/users.py,sha256=MKlmhDYRM7Yf-Trmi1ijEuqsDIUn326bdFADyDs7XYg,832
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scout/constants/__init__.py,sha256=
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scout/server/extensions/ldap_extension.py,sha256=nVgJ6YhSyvpg8J4bSYzJwoEvKhP0faWazt3Xk0ixE2U,2746
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scout_browser-4.103.0.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
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scout_browser-4.103.0.dist-info/licenses/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
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