chore(main): release 0.1.0

[varfish-bot]

:robot: I have created a release beep boop

0.1.0 (2024-05-16)

Features

• adapt filter frontend to case detail variant annotations (#1104) (#1122) (ed0652a)
• add a flag for incidental findings (#1121) (#1466) (04bd4f6)
• add api endpoints and front end for new qc data (#1144) (#1146) (62416c5)
• add cases_import settings for server to import from (#1020) (#1025) (b7b5f4c)
• add clear button for gene selection (#1580) (#1626) (6a308f5)
• add export for filter results to vue app (#866) (#876) (33755d9)
• add genome browser to case details and sv modal (#852) (#853) (28988cd)
• add seqmeta app to store available enrichment kits (#19) (#976) (a0a6cfb)
• add settings export and import to vue sv interface (#1453) (#1456) (6da6f43)
• add shortcut buttons for marking strucvars as artifact (#969) (#970) (d9e0b02)
• add support for importing per-case seqvar VCF (#1048) (#1155) (f2541e1)
• adding cases_qc app with initial support for Dragen QC (#1136) (9792b29)
• adding generic browser track capability and repeat tracks (#857) (38fcb98)
• adding models and APIs for cases_import app (#1021) (#1035) (5f847a5)
• adding persistent variant annotation (#1185) (#1198) (0b428a0)
• Adding presets to gene allowlist in vue filter app (#824) (#848) (e31ee43)
• adding support for cramino and ngs-bits QC (#1141) (#1143) (5cfec30)
• adding support for importing samtools/bcftools stats (#1139) (#1140) (7f03b6e)
• adjust varfish-server to unified gnomAD SV dbs (#1395) (#1397) (5f20f68)
• allow direct opening of variant details via results table (#1057) (#1081) (a7274fb)
• allow direct opening of variant details via results table (#871) (#1056) (1d91727)
• allow sorting by extra annotations (#1070) (#1074) (ee2d736)
• allow to see flags for same variant from other cases (#733) (#1531) (e5c12e4)
• allow using secret files for secrets (#1257) (#1258) (4ad84ac)
• AUTH parameters for TLS encrypted LDAP (#1245) (#1246) (9b5d507)
• bootstrapping cases_import app (#1019) (#1024) (e7d317e)
• bring over small variant details changes to SVs (#1089) (#1090) (56761c8)
• bump storybook version to 7 (#1091) (#1095) (bfec8a8)
• bump varfish server worker version to 0.5.0 (887) (#888) (afc4baf)
• bumping varfish-server-worker (#899) (#904) (a640fea)
• change label of final causativereported to final report (#665) (#1349) (b0bc5fc)
• change types of id column and sequence for large tables (#462) (#1350) (9d63c7c)
• display ClinVar and GTEx values for each gene (#672, #68) (#1129) (6c83a00)
• enable SpliceAI and CADD-PHRED columns if available (#1069) (#1073) (885bc13)
• flatten the "More..." tabs (#1059) (#1060) (7a828c5)
• implement expert load/save for genotype criteria (#872) (#875) (87f24b4)
• improving gene list display for many genes (#1092) (#1093) (d8785cb)
• indicate clicked variant when returning from variant details (#1526) (#1561) (c4bc4ef)
• integrate ClinGen, sHet, rCNV gene information (#1119) (1fbaf40)
• integrate seqvar details page from REEV (#1300) (#1369) (a8f6da1)
• integrate SV filtration by sv_type/tx impact (#986) (#995) (e9393b5)
• integrate variants/svs vuew apps into cases (#843) (#844) (e0f671b)
• integration of drf-spectacular for OpenAPI schema generation (#1405) (53a972a)
• integration of strucvars from REEV (#1300) (#1379) (c596e0c)
• integration of worker "seqvars ingest" (#1189) (ead404a)
• integration of worker "strucvars ingest" (#1190) (79cc5e7)
• interpret effective/compatible genotype info from worker (#861) (#865) (2178238)
• interpret SV breakpoint overlap with segmental duplications and repeats (#859) (#860) (a8e233c)
• keep table after viewing variant details and going back to the variant table (#1273) (#1464) (d1f793c)
• logging number of query result rows (#1066) (#1076) (d9c4e84)
• prepare backend for case detail variant annotations (#1099) (#1105) (28d18d2)
• prepare small variant models for storing results (#966) (#985) (939a046)
• provide genome browser through reverse proxy (#1011) (#1015) (1e21de3)
• remove necessity nltk data download (#1259) (#1269) (c10a37f)
• remove old filter features (#739) (#1628) (1ec5b3e)
• remove references to old hgnc gene table in varfish (#1551) (#1633) (dbe4fd4)
• removing old filter ui implementation (#864) (#880) (2dabbef)
• searching for cases only works with exact match (#1252) (#1270) (00edd75)
• separator for gene list or hpo terms (#1196) (#1480) (ba73b99)
• set default query preset for project (#1478) (#1611) (a1ab0ff)
• set default query preset for project (#1478) (#1622) (b28ca91)
• small variant artifact button should have hover description (#1118) (#1477) (64e979a)
• update SV filtration filters (#1094)) (#1098) (e0e3da2)
• upgrade to sodar core 0.13.0 (#1113) (#1114) (0111247)
• use annonars REST API services for small variant details (#1084) (#1087) (b7e8015)
• use CADD as default prioritization score (#1063) (#1075) (23fc1a3)
• viewing comments of variants in other samples (#964) (#1508) (bbd1348)
• vuejs switch from ag-grid to easy table (#961) (#965) (284c9d2)

Bug Fixes

• __vite_mapDeps not defined issue (#1373) (4b226f8)
• adapting strucvar details to latest annonars changes (#1229) (#1232) (b472a7c)
• add missing dependencies to Dockerfile (#996) (0fe8219)
• add missing labels in variant frequency details (#1064) (#1077) (1206181)
• add necessary tag for login page (#1012) (9a40f67)
• Add param to igv jump (#1406) (2903065)
• adding back default columns (#1127) (4fdc459)
• adding large panels causes incorrect linting errors (#1184) (#1250) (feb0885)
• adjust mt chromosome in igv calls (#1562) (#1563) (a28a279)
• adjusting frontend code to changes in backend (#1224, #1225) (#1228) (0537ed0)
• adjusting strucvar filter settings (#984) (94533b8)
• allow changing the number of rows and switching pages in structural variants table (#1268) (#1309) (5c964af)
• bump rfl to get bihealth/reev-frontend-lib#163 (#1422) (85f1725)
• bump rfl to get bihealth/reev-frontend-lib#164 (#1423) (c53a830)
• CADD score not shown in smallvar filter results vueapp (#890) (#920) (2508639)
• case details annotations tables unexpectedly empty in some cases (#1312) (#1313) (4d4fa10)
• case not set on result set creation (#1131) (2236a06)
• changed query presets only shown in filtering after page refresh (#1557) (#1624) (dc66b1a)
• cloning a user defined quick preset does not work (#1482) (#1625) (f0e2ea8)
• cnv, genotype criteria and quick presets (#858) (c6d5e96)
• color of sv flags does not depend on summary status (#1260) (#1325) (e5fb652)
• comments flags contains a perpetual spinning icon (#893) (#906) (1ec0be4)
• compatible with mehari 0.8 (#1174) (fe5a3dd)
• compound het and recessive mode broken (#1058) (#1078) (4b4da69)
• confusing genomic region genelist in filter vue app (#878, #879) (#882) (fc5e7cb)
• current state of special result set (#1377) (#1392) (5dbddde)
• dbsnp int to bigint (#1370) (baa17b0)
• deleting a case broken (#1162) (#1301) (0c2cf19)
• display of clinical significance in per-gene table (18c4a55)
• display of variant flagscommentsacmg counts are static always 0 (#1376) (#1437) (dbfd897)
• display SV gnomAD genomes counts, not exomes (#1424) (f87b46e)
• distance to next exon setting is not properly interpreted (#1029) (#1041) (1e5aaff)
• distance to next exon should be reset when selecting a new quick preset (#1256) (#1324) (432d6ce)
• effects all does not catch empty annotations (#1578) (#1579) (6b8fc34)
• enable strucvar view cards again (#1403) (cadd418)
• error in parsing chromosomal coordinates in genomic regions (#989) (#990) (37533d0)
• exomiser parameters are wrong (#947) (#1346) (0c3fb1c)
• exomiser prioritization broken for some genes (#1085) (#1086) (52063d1)
• fielderror cannot resolve keyword genotype into field (#988) (#991) (1e5a12b)
• file export mehari call is external (#1535) (#1536) (e662764)
• fix SV flagging issue with BND/INS types (#1088) (6a27732)
• further speed improvement loading small variant table (#1037) (#1038) (5fe0c36)
• gene allowlist validation inconsistent in front- and back-end (#1532) (#1538) (8917534)
• genomic regions are not stored correctly (#992) (#994) (b6a4955)
• genomic regions are not stored correctly (#992) (#999) (58a46ea)
• genotype criteria quick preset can now be applied (#856) (625cf68)
• high quality as default for sv filtration (#984) (#1027) (620eb8a)
• igv button creates new empty tab (#889) (#894) (98bf9ad)
• igv button in smallvariant results filter vue app (#877) (#881) (7737f24)
• igv linkout does not work for mitochondrial positions (#1283) (#1559) (1806783)
• igv shows error for grch38 svs (#1274) (#1323) (ac56b4e)
• issue with generating strucvar query JSON and empty values (#974) (f20877c)
• lift over orphaned variant annotations (#1124) (#1126) (764440a)
• limit seqvar details to gene from result row (#1380) (#1404) (a194921)
• make comments and flags work in SV filtration (#867) (#869) (7b1de6c)
• make flagging SVs possible again (#1006) (#1007) (cf9c1bb)
• make flags and comments for for SVs (#1401) (252ca55)
• make SV import work when feature-effects are empty (#1040) (3da4367)
• making gnomAD frequency display work again (#1108) (f92fb41)
• making IGV button in Vue.js SV filtration work (#870) (4f94a24)
• mehari call (#1199) (a43ebf4)
• mehari call (#1202) (2a9e3ba)
• misleading no available data message on empty result sets (#1275) (#1310) (2b16503)
• optional columns selected with each variant detail view (#1111) (#1112) (3a49d08)
• order link-outs alphabetically (#1097) (e3a7043)
• permissions broken for smallvariant query (#1013) (#1014) (5bf6b4d)
• phenotype score not shown in vue filter results (#892) (#921) (943a6e5)
• phenotype scoring in vue filter app broken (#924) (#925) (3b82979)
• previous query is not restricted to user (#1030) (#1080) (58ff28f)
• prioritizer and phenotype scoring not used in query (#1016) (#1017) (69fd67a)
• prioriziation with hpo terms not accepting omim terms (#902) (#903) (1ad920b)
• prioriziation with hpo terms not accepting omim terms pt2 (#907) (#908) (aa18371)
• properly handle all-null/"." REVEL etc. scores (#1117) (#1130) (10afced)
• properly link out in SV results table (#1068) (#1072) (5ecd0cc)
• properly load user annotations into stores (#1197) (6bc4172)
• properly reset factoryboy sequences when used with snapshot tests (#1186) (0f641a2)
• QC missing alignment quality in case detail vue app (#922) (#929) (8b6916a)
• query preset cannot add gene regions presets (#1166) (#1457) (6bc5bfb)
• query preset removing a quick preset does not remove preset (#1165) (#1458) (e90e3a1)
• query presets cannot add new quick preset (#1164) (#1459) (39603c9)
• query presets cannot add new quick preset (#1164) (#1460) (e56ad93)
• query result sets not created on case import (#1241) (#1242) (b5659a9)
• quick preset dropdown is empty in vue app (#891) (#896) (970edd7)
• quick preset dropdown is empty in vue app (#900) (#901) (bce57c6)
• quick presets in vue filter app (#849) (#862) (1e956c9)
• re-enable searching for cases and list in project overview (#1004) (#1008) (8679d52)
• Remove IGV prefixing (#1284) (3a917fe)
• removing dedup/repeat filter for SVs again (#897) (#915) (7ea4f6c)
• replace jannovar call in file export with mehari (#1463) (#1512) (82235b8)
• resolve issue in project QC with variant statistics API (#1009) (a1188a8)
• resolve issue with sv quick preset initialization (#1003) (864029a)
• resolve pylance issue with subscription of dict (#1187) (3a7fbe0)
• resolving issues after large-scale update (#1107) (4fe2a54)
• result download broken in vue app for scores (#926) (#927) (5a46eeb)
• resultset store issue (#1209) (e56eac7)
• returning from sv details shows wrong result set (#1438) (#1439) (1a8459d)
• rollback mehari call (#1204) (1ce636b)
• small variant and svs load all available flags and comments (#1032) (#1036) (6bc445b)
• sorting broken in smallvariant results table (#1018) (#1026) (ddae17a)
• special result row set not updating when flags are updated (#1378) (#1398) (d7ab728)
• structural variant worker call (#1203) (d752480)
• strucvar filtration always run with grch37 (#1271) (#1272) (c0a8fbc)
• suppress BAM QC table if BAM stats missing (#1213) (6f0cfa0)
• sv queries submit to wrong celery worker queue (#1052) (#1053) (e12b02d)
• sv results page shows previous results after sv details (#1302) (#1303) (028e6e5)
• switch case import data port setting to type integer (#1214) (ac9bb76)
• table in default sorting after returning from details (#1109) (#1110) (7b346d4)
• table sorting on variants result page (#1128) (1f3e4a2)
• table sorting settings not preserved (#1212) (0157ea1)
• timing issue when initializing pinia (#1374) (64c99e6)
• update reev frontend lib for mt igv issue (#1575) (#1576) (eca30d3)
• updated pipfile lock (#1210) (6ab8ff5)
• updating Pipfile.lock (#1054) (#1055) (fe64118)
• value in exon max dist prevents submitting query (#993) (#1005) (682a4c6)
• variant details not working for grch38 (#1509) (#1524) (efeba9f)
• variant icons leads to wrong postion on variant details page (#1315) (#1465) (9d3d83b)
• vue app queries using virtual panels can't be submitted (#940) (#944) (c36bb30)
• vue linkout pubmed+pheno currently disabled (#941) (#945) (6d0b2e1)
• vue small variant details genotype info is empty (#932) (#946) (041a036)
• vue small variants extra annotations are missing (#931) (#943) (b4f98bb)
• vuejs case disease terms not editable (#948) (#949) (c6be021)
• vuejs make filter button text more descriptive (#939) (#958) (e380a19)
• vuejs varsome linkout for variants missing (#951) (#956) (1119c56)
• whole transcript preset should include non coding transcripts (#1044) (#1071) (36e8055)
• wrong genome build for igv visualization of sv (#1511) (#1558) (6b1d6c9)
• xlsx file export issues (#1504) (#1505) (145e8b4)

Reverts

• quick preset dropdown is empty in vue app (#891) (#896) (6bb0302)

Documentation

• fix admin_ingest.rst (#917) (3be1971)
• fixing readthedocs documentation (#1317) (575a946)
• small fixes to admin ingest (#918) (f3f13bb)

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