scout-browser 4.99.0__py3-none-any.whl → 4.100.0__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 +30 -15
- scout/adapter/mongo/clinvar.py +23 -31
- scout/adapter/mongo/event.py +14 -4
- scout/adapter/mongo/omics_variant.py +14 -1
- scout/adapter/mongo/query.py +24 -1
- scout/adapter/mongo/variant.py +37 -19
- scout/adapter/mongo/variant_loader.py +159 -176
- scout/build/individual.py +3 -1
- scout/commands/download/ensembl.py +1 -2
- scout/commands/load/research.py +2 -3
- scout/commands/update/individual.py +1 -0
- scout/constants/__init__.py +7 -2
- scout/constants/igv_tracks.py +4 -3
- scout/constants/indexes.py +5 -4
- scout/constants/query_terms.py +1 -0
- scout/models/case/case.py +1 -0
- scout/models/case/case_loading_models.py +3 -1
- scout/parse/ensembl.py +8 -3
- scout/server/app.py +6 -0
- scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html +10 -0
- scout/server/blueprints/cases/controllers.py +9 -3
- scout/server/blueprints/cases/templates/cases/case_report.html +25 -13
- scout/server/blueprints/cases/templates/cases/chanjo2_form.html +1 -1
- scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html +1 -1
- scout/server/blueprints/cases/templates/cases/gene_panel.html +1 -1
- scout/server/blueprints/cases/templates/cases/utils.html +19 -0
- scout/server/blueprints/clinvar/controllers.py +5 -1
- scout/server/blueprints/clinvar/templates/clinvar/clinvar_submissions.html +34 -12
- scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html +1 -1
- scout/server/blueprints/diagnoses/static/diagnoses.js +8 -1
- scout/server/blueprints/institutes/static/variants_list_scripts.js +9 -1
- scout/server/blueprints/institutes/templates/overview/institute_sidebar.html +9 -1
- scout/server/blueprints/mme/__init__.py +1 -0
- scout/server/blueprints/mme/controllers.py +18 -0
- scout/server/blueprints/mme/templates/mme/mme_submissions.html +153 -0
- scout/server/blueprints/mme/views.py +34 -0
- scout/server/blueprints/panels/templates/panels/panel.html +19 -6
- scout/server/blueprints/phenotypes/templates/phenotypes/hpo_terms.html +8 -1
- scout/server/blueprints/variant/controllers.py +19 -10
- scout/server/blueprints/variant/templates/variant/acmg.html +9 -0
- scout/server/blueprints/variant/templates/variant/cancer-variant.html +1 -1
- scout/server/blueprints/variant/templates/variant/components.html +19 -16
- scout/server/blueprints/variant/templates/variant/sv-variant.html +2 -2
- scout/server/blueprints/variant/templates/variant/utils.html +20 -8
- scout/server/blueprints/variant/templates/variant/variant.html +42 -1
- scout/server/blueprints/variant/views.py +12 -0
- scout/server/blueprints/variants/controllers.py +17 -9
- scout/server/blueprints/variants/forms.py +8 -3
- scout/server/blueprints/variants/templates/variants/components.html +8 -2
- scout/server/blueprints/variants/templates/variants/indicators.html +11 -13
- scout/server/blueprints/variants/templates/variants/utils.html +28 -23
- scout/server/extensions/bionano_extension.py +0 -1
- scout/server/extensions/chanjo2_extension.py +54 -13
- scout/server/links.py +15 -0
- scout/server/static/bs_styles.css +34 -6
- scout/server/templates/utils.html +9 -10
- scout/server/utils.py +18 -0
- scout/utils/ensembl_biomart_clients.py +1 -0
- scout/utils/scout_requests.py +1 -3
- {scout_browser-4.99.0.dist-info → scout_browser-4.100.0.dist-info}/METADATA +1 -1
- {scout_browser-4.99.0.dist-info → scout_browser-4.100.0.dist-info}/RECORD +64 -60
- {scout_browser-4.99.0.dist-info → scout_browser-4.100.0.dist-info}/WHEEL +0 -0
- {scout_browser-4.99.0.dist-info → scout_browser-4.100.0.dist-info}/entry_points.txt +0 -0
- {scout_browser-4.99.0.dist-info → scout_browser-4.100.0.dist-info}/licenses/LICENSE +0 -0
@@ -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=BImiGlUE7pRuXY-CUg5CENuSfM3TVJxNgvQSAJQ1-KY,66015
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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=e11k6mkJNjGOAENx9vaXGl8SOWM88Q8e8qtShxeFzuE,19521
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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=xC6VdfZUU8tIPKZrCklD-zX3wgfZD09ze5wrpyLbkIA,20245
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scout/adapter/mongo/filter.py,sha256=rIdjiDJCrNDeTNgssKm7n1HTxne72jvlX2I3FQjQGo8,9687
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scout/adapter/mongo/hgnc.py,sha256=P80WdIFkpFDeR6Pa0H-pgeScGrZdCviWVL4rqR5Aqvk,16547
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scout/adapter/mongo/hpo.py,sha256=ps2Pix3sGeea7DenboZVP5j7Vh9WAgX3-sgpbAj0Eck,6871
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@@ -19,23 +19,23 @@ scout/adapter/mongo/index.py,sha256=TZPVv6xBWsEtZpBUWp5uhjuPjQMfVss4lZZju49g1Lw,
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scout/adapter/mongo/institute.py,sha256=SaA1mRxIZHtMfriMnd0yKiup-xSAG5g0ry9Achra9Tk,6646
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scout/adapter/mongo/managed_variant.py,sha256=mPbp64nMDwAij8zvBbFGjI3MLbk6CC-OO9RTwtEIi44,8451
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scout/adapter/mongo/matchmaker.py,sha256=amTvFOlUbrt1RmecY_8hPY6bO3j79lc2UbmzlCQcRuk,6378
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scout/adapter/mongo/omics_variant.py,sha256=
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scout/adapter/mongo/omics_variant.py,sha256=0KuzCEsmxXDNgD3rgrwWT-mUANP3sdhl_Ekv2wIDGrU,8539
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scout/adapter/mongo/panel.py,sha256=d1oMEYAiDGybLmlbbf3-fQdCdU0-T7x2XdIUwZGthYk,20031
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scout/adapter/mongo/phenomodel.py,sha256=cypSS8YRzu98Bf1kC0orfrLNn_ZQSYCK8e4mNR5PaPY,2572
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scout/adapter/mongo/query.py,sha256=
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scout/adapter/mongo/query.py,sha256=zXAT5lWadRbhCNw5w161uCKzoUyTuUSlCm32P8aBa_M,36315
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scout/adapter/mongo/rank_model.py,sha256=wvDNI4OLf-f7ZYZ_Q_6qi0myxOJCNNJR_-2-_0u2K2M,5712
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scout/adapter/mongo/transcript.py,sha256=3U1qtyxZ1DnrzdBJm_emJXISMYFKJuX_zAKynUt8NMY,7417
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scout/adapter/mongo/user.py,sha256=QoQnRWqi_dV3ZwGzBonEU6Ap9TgMDf2x_C5UIqG0pa0,2569
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scout/adapter/mongo/variant.py,sha256=
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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=8fBEA_SrBJcvDgF5tceYfMQNnZTt6hwM4zcTjOUeRO0,28397
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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/ccv.py,sha256=cfAWSQ5cSBWURkL9_fPm1Y5aRcTIDOE9ieSWaYLufB4,1660
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scout/build/disease.py,sha256=Zew9AF_z1NbbKcO3uJZ2wgni501SkfnYRgnaCZ4m8FY,2020
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scout/build/hpo.py,sha256=LJBCTq-x09D0CSKcUHB8a6ynuUrVh_7Ia0ooA1BxMys,1207
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scout/build/individual.py,sha256=
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scout/build/individual.py,sha256=2EBcuh23xUDeP2F5kVPAh1cAoGp_xMpFXEbSBmyxeG8,5310
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scout/build/institute.py,sha256=CZKn-cFbh0cWO2ySoRV_P1nYFizlyvu50LKrtAz-PLo,1330
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scout/build/managed_variant.py,sha256=krcQBc4LLxlnUQwXuV2FxNLiSkMoIkLxQueYFl04Vyo,1666
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scout/build/panel.py,sha256=smhtynG_ggNgUyuAGqg_-m1UMnBHhrk2ALutYoNTTec,4273
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@@ -62,7 +62,7 @@ scout/commands/delete/__init__.py,sha256=6Z97FsWMqyKqF64Anl1zwljVNTfjJUCI7yylxIE
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scout/commands/delete/delete_command.py,sha256=c-cWdtc0VCLVLL5hpMxSuyaBiYCppm403eRoLhD1SSo,14568
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scout/commands/download/__init__.py,sha256=mfDzxqKzJ0LgfPBN_fehkdX5BPy1FJ3rauA3ORLIjCM,39
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scout/commands/download/download_command.py,sha256=m5CKefst3qhs4urfNu1A2TERisUb_5WPn-wn9bGCDr0,736
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scout/commands/download/ensembl.py,sha256=
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scout/commands/download/ensembl.py,sha256=_kdtL3B2fdW-ntmOU1QpFw1ji8ysHSLdDsBXGtCiyVU,2631
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scout/commands/download/everything.py,sha256=KJ0xKeIx7Rtxv38XRE2RVYBTqec9UXh6LKrozj_6Mwo,1426
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scout/commands/download/exac.py,sha256=Hy-RKnjlPRvvMgkExpyrxdjFXW_kPUvS012SyqYp41E,1052
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scout/commands/download/hgnc.py,sha256=Htp0uOhHDAqSrfIG7xRg2WE8ZKO00chOwW1xqv-OzC8,890
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@@ -91,7 +91,7 @@ scout/commands/load/institute.py,sha256=EYbDeWmpeRl0_jBnsckAp6qua5VyZKpczoHfADfY
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scout/commands/load/panel.py,sha256=kx6HpFYcYgPwTLsgarjM7eL43bkZwpPj__I_gqjGN60,2925
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scout/commands/load/region.py,sha256=psICLlMf5WBdSCgXsJZUsM8fICsTJB3Q6U6dB5S6w_8,869
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scout/commands/load/report.py,sha256=DrnyOJcLbOUUJHzI3jwlj955zYohvjuTeeoeUS_ZU8Q,3564
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scout/commands/load/research.py,sha256=
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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/setup/__init__.py,sha256=uiuizwirbfLqp93K4__b982obk1stkzwpvXHi51OAbE,31
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@@ -103,7 +103,7 @@ scout/commands/update/compounds.py,sha256=vwCtb6045tGovKWHqY_uL8w1l9rZ_Hxlt0gUU0
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scout/commands/update/disease.py,sha256=AajPLoEtd9YeU3jf7S7ZQRs3_o1H3GSxHsST_sVaIZQ,3846
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scout/commands/update/genes.py,sha256=GhYIn2zWrAZMhdJjzzrpo8AquFqr7XOvosOk8lg4Zwk,6989
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scout/commands/update/hpo.py,sha256=eyCuUlUwPmyP0oLh1olXhdqInlUXDdLe8ylgTlHWi-g,1339
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scout/commands/update/individual.py,sha256=
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scout/commands/update/individual.py,sha256=GwhS7P_1PUnUMYDF77Nsez7Vn212JU3cgN-qHRABk8I,4201
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scout/commands/update/institute.py,sha256=ms8mmTGfCXqxeh_vSB1cdNDGrdHoSSgh9ryhB5GrJQc,1727
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scout/commands/update/omim.py,sha256=s39qterBGhtBfW7Uc-IJabni93PIhT8shqVbkmQBb9k,2309
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scout/commands/update/panel.py,sha256=990shZ15k5pwHUkd767o8oQ5iqVIpgRA7N_9yv1_eqc,2912
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@@ -125,7 +125,7 @@ scout/commands/view/intervals.py,sha256=8Pofxy0DwL2Euh3SdnTLLWsU6DjLNOwIGdxeCS83
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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/constants/__init__.py,sha256=F17Q75A0RkvYzXujvqjwP5N2nXKVsIGu5UF1wI8_dYw,5951
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scout/constants/acmg.py,sha256=N9X2sJLbK6g6tDPhW0gYQifImzaowb4F6jfTYUBr-Z0,18717
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scout/constants/case_tags.py,sha256=O-BwEzU36MSpN7qqd-aSvoi4-VDRY8rM5hQ7Jg7DMgs,9447
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scout/constants/ccv.py,sha256=YP82qWCrjv3JB8d2LkUdBlBZolk0uF3nhNmkNgmebiI,9734
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scout/constants/file_types.py,sha256=9nHBnknssjdQnHm8jA8MoWAJq1shS4h5apyC9zwGCc0,2890
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scout/constants/filters.py,sha256=ZgVGt6No5D7PiN1o1wWDm3E5SCRk7YLya87_4QtIMPs,979
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scout/constants/gene_tags.py,sha256=yBrMu9qXyYaQ13l3XMakooyd2ZtPXm1XgpSSH_bC-5U,4513
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scout/constants/igv_tracks.py,sha256=584SdO6qJHAcfCxHJQaM4YAnzu4M_uviJIUg6gt_jok,4675
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scout/constants/indexes.py,sha256=qe-1ntYqlwqLEDqsJDX6RhAnCYt_2tVZ9ZJ4nWoTIkQ,5843
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scout/constants/panels.py,sha256=1N2Ys94IxoEWxySTJDW-rFJ55vtCkqnn6bRWjkw61J4,876
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scout/constants/phenotype.py,sha256=MrbXirisR_7GPnxV3NOj3-BoM9CvtGgFZj7PfJu85RM,2331
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scout/constants/query_terms.py,sha256=tuHYdV0nNKCw4UpypOwUgKImaWFimOyn-evAEGdxz-E,1615
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scout/constants/so_terms.py,sha256=aJcQv3wgpZylVhqSJH854WS8xSARDxWGnW6I5mG1egE,4321
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scout/constants/variant_tags.py,sha256=NnpcJGRDycq3PIrDQsd57ynJ8NzmJETICBVjzGKZlSg,17907
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scout/constants/variants_export.py,sha256=uQvFsbRMdbgl39HUdGWzFAEe1KOHp5OgvhjbGMD3O_Q,1969
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scout/models/case/__init__.py,sha256=Sqczn7Wm9KYZtPGAHCvwX_6j9vlaK-0myJtSDlS-448,121
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scout/models/case/case.py,sha256=y4Ympv0YvBJQDqeRcRDwZoQCHLwsr2o1YmYjkk89Nb0,5351
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scout/models/case/case_loading_models.py,sha256=J5TdlzW3SrpZiuDYf06DhXUXFG2NkuKrZJlINOqxwj0,22224
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scout/models/variant/__init__.py,sha256=H-IZ2hSTSVS28S8FZzA8j2Cyu1PHQFXyMWJFtCucPAk,40
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scout/models/variant/gene.py,sha256=98CG_JcAklGGFIrUulf1_olQalV65kXQO-gOf7VQZ0A,1095
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scout/server/static/humans.txt,sha256=UdqAR07_5LAWWfgH2Ty4RR8BhoHS1WXpx9euKtXqqhs,259
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scout_browser-4.100.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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scout_browser-4.100.0.dist-info/licenses/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
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