# Changelog ## [0.17.0](https://github.com/varfish-org/varfish-server-worker/compare/v0.16.1...v0.17.0) (2024-10-30) ### Features * inhouse freqs useable in seqvars query ([#232](https://github.com/varfish-org/varfish-server-worker/issues/232)) ([#522](https://github.com/varfish-org/varfish-server-worker/issues/522)) ([45bec0c](https://github.com/varfish-org/varfish-server-worker/commit/45bec0c23389644f2446767d4dcba25a36d4ab9c)) ## [0.16.1](https://github.com/varfish-org/varfish-server-worker/compare/v0.16.0...v0.16.1) (2024-10-30) ### Bug Fixes * seqvars aggregate async runtime error ([#519](https://github.com/varfish-org/varfish-server-worker/issues/519)) ([#520](https://github.com/varfish-org/varfish-server-worker/issues/520)) ([3911afe](https://github.com/varfish-org/varfish-server-worker/commit/3911afe64aec4e38ead6ae458c2fcc69f8ee08a8)) ## [0.16.0](https://github.com/varfish-org/varfish-server-worker/compare/v0.15.0...v0.16.0) (2024-10-28) ### ⚠ BREAKING CHANGES * adjusting max_af to max_carriers for inhouse ([#512](https://github.com/varfish-org/varfish-server-worker/issues/512)) * more protobuf cleaning ([#511](https://github.com/varfish-org/varfish-server-worker/issues/511)) ### Code Refactoring * adjusting max_af to max_carriers for inhouse ([#512](https://github.com/varfish-org/varfish-server-worker/issues/512)) ([c212b44](https://github.com/varfish-org/varfish-server-worker/commit/c212b44656ee2b4f3e1eecd7f58ceb16b6577ca3)) * consolidating protobuf definitions ([#508](https://github.com/varfish-org/varfish-server-worker/issues/508)) ([#509](https://github.com/varfish-org/varfish-server-worker/issues/509)) ([0edcf98](https://github.com/varfish-org/varfish-server-worker/commit/0edcf9875a66a881803c0f9d842fae1e95af05f2)) * more protobuf cleaning ([#511](https://github.com/varfish-org/varfish-server-worker/issues/511)) ([06ebb8a](https://github.com/varfish-org/varfish-server-worker/commit/06ebb8a3354f22f6e0ac1f5950e5714e97fd4be3)) ## [0.15.0](https://github.com/varfish-org/varfish-server-worker/compare/v0.14.0...v0.15.0) (2024-10-24) ### Features * adding more annotations to output ([#504](https://github.com/varfish-org/varfish-server-worker/issues/504)) ([#505](https://github.com/varfish-org/varfish-server-worker/issues/505)) ([0225f81](https://github.com/varfish-org/varfish-server-worker/commit/0225f81e5b159868fd76154e9bfd7fdde2919ad7)) ### Bug Fixes * typos in score field names ([#507](https://github.com/varfish-org/varfish-server-worker/issues/507)) ([85da7e6](https://github.com/varfish-org/varfish-server-worker/commit/85da7e6f8838523a67b98a5b937efc195f682857)) ## [0.14.0](https://github.com/varfish-org/varfish-server-worker/compare/v0.13.2...v0.14.0) (2024-10-09) ### Features * add mode of inheritance from HPO ([#493](https://github.com/varfish-org/varfish-server-worker/issues/493)) ([2da2b86](https://github.com/varfish-org/varfish-server-worker/commit/2da2b862bf5be6782c7cea265481b8b5650499e5)) ### Bug Fixes * bump mehari to escape clinvar output string ([#485](https://github.com/varfish-org/varfish-server-worker/issues/485)) ([#488](https://github.com/varfish-org/varfish-server-worker/issues/488)) ([e0e2370](https://github.com/varfish-org/varfish-server-worker/commit/e0e2370f27b6d1a296272b90138df6ab3a5f4688)) * suppress unknown consequence errors ([#491](https://github.com/varfish-org/varfish-server-worker/issues/491)) ([c95ed79](https://github.com/varfish-org/varfish-server-worker/commit/c95ed797d0c3354684be338e33970ba090c5873d)) * suppress unknown consequence errors ([#492](https://github.com/varfish-org/varfish-server-worker/issues/492)) ([bfe718d](https://github.com/varfish-org/varfish-server-worker/commit/bfe718dd8b6927d91a295a2006506fcf161da700)) ## [0.13.2](https://github.com/varfish-org/varfish-server-worker/compare/v0.13.1...v0.13.2) (2024-10-07) ### Bug Fixes * anc can be float or int ([#478](https://github.com/varfish-org/varfish-server-worker/issues/478)) ([0c37d30](https://github.com/varfish-org/varfish-server-worker/commit/0c37d30ae12adbd640df77373c8d517301e54c9c)) ## [0.13.1](https://github.com/varfish-org/varfish-server-worker/compare/v0.13.0...v0.13.1) (2024-10-07) ### Bug Fixes * add missing consequence conversion ([#454](https://github.com/varfish-org/varfish-server-worker/issues/454)) ([843922a](https://github.com/varfish-org/varfish-server-worker/commit/843922ae6ac9ec364459406e6c3770da607b6011)) * changing protobuf and others as needed ([#455](https://github.com/varfish-org/varfish-server-worker/issues/455)) ([2718a6e](https://github.com/varfish-org/varfish-server-worker/commit/2718a6ed26b093a63b08fc8dbdbf65812028e3a6)) * make reading from S3 work and bump mehari ([#452](https://github.com/varfish-org/varfish-server-worker/issues/452)) ([13a106a](https://github.com/varfish-org/varfish-server-worker/commit/13a106a080577ba094f4cfed616b1d5ab65d2228)) * proper handling of FORMAT/amq ([#477](https://github.com/varfish-org/varfish-server-worker/issues/477)) ([e1f89a0](https://github.com/varfish-org/varfish-server-worker/commit/e1f89a0f295780a6a1418f185cb36e0e4968e68e)) ## [0.13.0](https://github.com/varfish-org/varfish-server-worker/compare/v0.12.0...v0.13.0) (2024-08-06) ### ⚠ BREAKING CHANGES * write out hom. ref. count in seqvars aggregate ([#428](https://github.com/varfish-org/varfish-server-worker/issues/428)) (#429) * cleanup protobufs to best practices ([#423](https://github.com/varfish-org/varfish-server-worker/issues/423)) (#425) * refactory query schema to use protobuf ([#374](https://github.com/varfish-org/varfish-server-worker/issues/374)) (#419) ### Features * cleanup protobufs to best practices ([#423](https://github.com/varfish-org/varfish-server-worker/issues/423)) ([#425](https://github.com/varfish-org/varfish-server-worker/issues/425)) ([48a3144](https://github.com/varfish-org/varfish-server-worker/commit/48a3144c680a97ec32db12c7b00e7add2bf51899)) * introduce protobuf schema for seqvars query output ([#375](https://github.com/varfish-org/varfish-server-worker/issues/375)) ([#430](https://github.com/varfish-org/varfish-server-worker/issues/430)) ([214c8e9](https://github.com/varfish-org/varfish-server-worker/commit/214c8e95aff950a131f158542c22c5911f5f6eef)) * message members explicitely optional for protobufs ([#431](https://github.com/varfish-org/varfish-server-worker/issues/431)) ([1458aad](https://github.com/varfish-org/varfish-server-worker/commit/1458aad8346a2b154fa37fcbef41da075a73530b)) * refactory query schema to use protobuf ([#374](https://github.com/varfish-org/varfish-server-worker/issues/374)) ([#419](https://github.com/varfish-org/varfish-server-worker/issues/419)) ([0e14e16](https://github.com/varfish-org/varfish-server-worker/commit/0e14e16df4816e5ae01494db5437b7de50acb0a6)) * write out hom. ref. count in seqvars aggregate ([#428](https://github.com/varfish-org/varfish-server-worker/issues/428)) ([#429](https://github.com/varfish-org/varfish-server-worker/issues/429)) ([3830a55](https://github.com/varfish-org/varfish-server-worker/commit/3830a552bf1baa175d17007d429e10184ad82004)) ### Bug Fixes * allow parsing FORMAT/anc as Float/f32 ([#414](https://github.com/varfish-org/varfish-server-worker/issues/414)) ([bf4634b](https://github.com/varfish-org/varfish-server-worker/commit/bf4634b0cb93c77126638d272cb591005ec8b1b3)) ## [0.12.0](https://github.com/varfish-org/varfish-server-worker/compare/v0.11.0...v0.12.0) (2024-06-19) ### Features * implement file identifier mappings ([#364](https://github.com/varfish-org/varfish-server-worker/issues/364)) ([#365](https://github.com/varfish-org/varfish-server-worker/issues/365)) ([57db49a](https://github.com/varfish-org/varfish-server-worker/commit/57db49a6f67daa2d69fa24fc1eb887937a390fd8)) ### Bug Fixes * noodles and other deps ([#378](https://github.com/varfish-org/varfish-server-worker/issues/378)) ([#379](https://github.com/varfish-org/varfish-server-worker/issues/379)) ([4dc0f94](https://github.com/varfish-org/varfish-server-worker/commit/4dc0f94d33c0bf3ade90eeef42e7c2e367146dde)) * using custom S3 endpoint ([#362](https://github.com/varfish-org/varfish-server-worker/issues/362)) ([06334e6](https://github.com/varfish-org/varfish-server-worker/commit/06334e66875699e2ad182bb3c3e366bcf3d56c0b)) ## [0.11.0](https://github.com/varfish-org/varfish-server-worker/compare/v0.10.2...v0.11.0) (2024-02-27) ### Features * add build of docker containers ([#243](https://github.com/varfish-org/varfish-server-worker/issues/243)) ([c455e25](https://github.com/varfish-org/varfish-server-worker/commit/c455e257af57b6d100c2f96c1c5633b39910e1a2)) * adding "seqvars aggregate" command ([#211](https://github.com/varfish-org/varfish-server-worker/issues/211)) ([#214](https://github.com/varfish-org/varfish-server-worker/issues/214)) ([d6db0b7](https://github.com/varfish-org/varfish-server-worker/commit/d6db0b7ab2fb17987d1052c0c7bba1113d34d025)) * adjust "strucvars query" to read ingested VCFs ([#202](https://github.com/varfish-org/varfish-server-worker/issues/202)) ([#220](https://github.com/varfish-org/varfish-server-worker/issues/220)) ([1fb3c58](https://github.com/varfish-org/varfish-server-worker/commit/1fb3c581e58d017923b1f8261f9e12515e0a648a)) * allow importing gnomAD SV/CNV v4 as background db ([#295](https://github.com/varfish-org/varfish-server-worker/issues/295)) ([#310](https://github.com/varfish-org/varfish-server-worker/issues/310)) ([ce9b391](https://github.com/varfish-org/varfish-server-worker/commit/ce9b39149e68c005b4a4abf250a9671a141a17a5)) * create .tbi for written .vcf.gz files ([#233](https://github.com/varfish-org/varfish-server-worker/issues/233)) ([#241](https://github.com/varfish-org/varfish-server-worker/issues/241)) ([be99642](https://github.com/varfish-org/varfish-server-worker/commit/be99642d88946c5c45666aa4dc6716b5267796ce)) * implement "seqvars ingest" command ([#199](https://github.com/varfish-org/varfish-server-worker/issues/199)) ([#206](https://github.com/varfish-org/varfish-server-worker/issues/206)) ([21b965c](https://github.com/varfish-org/varfish-server-worker/commit/21b965c7bf9d0d54fcbc3d91ee8d9c007ec6ca60)) * implement "seqvars query" command ([#201](https://github.com/varfish-org/varfish-server-worker/issues/201)) ([#223](https://github.com/varfish-org/varfish-server-worker/issues/223)) ([a7cb0bd](https://github.com/varfish-org/varfish-server-worker/commit/a7cb0bdf96ad61ce2b044535b2f1e5657875240b)) * implement "strucvars ingest" command ([#200](https://github.com/varfish-org/varfish-server-worker/issues/200)) ([#208](https://github.com/varfish-org/varfish-server-worker/issues/208)) ([a783ef3](https://github.com/varfish-org/varfish-server-worker/commit/a783ef3ab08f103435799345d738ae723bf9997f)) * implement I/O from/to S3 ([#234](https://github.com/varfish-org/varfish-server-worker/issues/234)) ([#242](https://github.com/varfish-org/varfish-server-worker/issues/242)) ([414bb5d](https://github.com/varfish-org/varfish-server-worker/commit/414bb5d468eacda8ca68b3cb778ae8bf5f5dd0c2)) * implement ingest and aggregate for sniffles2 ([#296](https://github.com/varfish-org/varfish-server-worker/issues/296)) ([#312](https://github.com/varfish-org/varfish-server-worker/issues/312)) ([6432365](https://github.com/varfish-org/varfish-server-worker/commit/6432365727b87e51b5fd7b803a5c700ac2cb3167)) * implement ingest for Clair3+GLNexus ([#297](https://github.com/varfish-org/varfish-server-worker/issues/297)) ([#311](https://github.com/varfish-org/varfish-server-worker/issues/311)) ([4144003](https://github.com/varfish-org/varfish-server-worker/commit/4144003726a0dd73d9b87294cf178666383382b0)) * implement parsing of clinvar-data-jsonl data ([#198](https://github.com/varfish-org/varfish-server-worker/issues/198)) ([#204](https://github.com/varfish-org/varfish-server-worker/issues/204)) ([e0ea7ac](https://github.com/varfish-org/varfish-server-worker/commit/e0ea7ac1b959c035691d957ea619739dc3e7d619)) * implementing "seqvars prefilter" ([#209](https://github.com/varfish-org/varfish-server-worker/issues/209)) ([#213](https://github.com/varfish-org/varfish-server-worker/issues/213)) ([984dc8b](https://github.com/varfish-org/varfish-server-worker/commit/984dc8b01fa552ee8972a170fd7b431c3424a522)) * remove gene regions from "strucvars query" database enhancement ([#221](https://github.com/varfish-org/varfish-server-worker/issues/221)) ([#222](https://github.com/varfish-org/varfish-server-worker/issues/222)) ([28663b6](https://github.com/varfish-org/varfish-server-worker/commit/28663b6feca424514dd422d3ce0ac2e61d573d75)) * transform "db mk-inhouse" to "strucvars aggregate" ([#212](https://github.com/varfish-org/varfish-server-worker/issues/212)) ([#217](https://github.com/varfish-org/varfish-server-worker/issues/217)) ([b51f027](https://github.com/varfish-org/varfish-server-worker/commit/b51f027918a57e1402e825a00487bb53d1440fd8)) * transform "db to-bin" to "strucvars txt-to-bin" ([#218](https://github.com/varfish-org/varfish-server-worker/issues/218)) ([#219](https://github.com/varfish-org/varfish-server-worker/issues/219)) ([ea6e387](https://github.com/varfish-org/varfish-server-worker/commit/ea6e387b87e51b38b49a93ce2a90e52109f71df5)) * unify database names in strucvar filtration ([#307](https://github.com/varfish-org/varfish-server-worker/issues/307)) ([#308](https://github.com/varfish-org/varfish-server-worker/issues/308)) ([43413d4](https://github.com/varfish-org/varfish-server-worker/commit/43413d4e5bc7f548756a7f5e064dd7bccd12593f)) * write out fileDate on ingest ([#210](https://github.com/varfish-org/varfish-server-worker/issues/210)) ([#215](https://github.com/varfish-org/varfish-server-worker/issues/215)) ([7731958](https://github.com/varfish-org/varfish-server-worker/commit/7731958a4b274db604bb7d88c5a5d501bd8b7390)) ### Bug Fixes * normalize patho-mms.bed => patho_mms.bed ([#315](https://github.com/varfish-org/varfish-server-worker/issues/315)) ([48afb7d](https://github.com/varfish-org/varfish-server-worker/commit/48afb7df19810699d95457778ac87cae8764e27e)) ### [0.10.2](https://www.github.com/bihealth/varfish-server-worker/compare/v0.10.1...v0.10.2) (2023-10-04) ### Bug Fixes * resolve prost from_i32 deprecation ([#193](https://www.github.com/bihealth/varfish-server-worker/issues/193)) ([fc4cd3e](https://www.github.com/bihealth/varfish-server-worker/commit/fc4cd3ef8591b43978340b9b6c37c488fdddc9be)) ### [0.10.1](https://www.github.com/bihealth/varfish-server-worker/compare/v0.10.0...v0.10.1) (2023-07-31) ### Bug Fixes * allow HGNC IDs in gene allow list ([#153](https://www.github.com/bihealth/varfish-server-worker/issues/153)) ([416bf28](https://www.github.com/bihealth/varfish-server-worker/commit/416bf2823af6147fddf73a43532491a3da396947)) ## [0.10.0](https://www.github.com/bihealth/varfish-server-worker/compare/v0.9.0...v0.10.0) (2023-07-25) ### Features * write out HGNC ids for sv query results ([#150](https://www.github.com/bihealth/varfish-server-worker/issues/150)) ([#151](https://www.github.com/bihealth/varfish-server-worker/issues/151)) ([9e1074b](https://www.github.com/bihealth/varfish-server-worker/commit/9e1074b53572cf73344b3ac40e412d3d12f9f882)) ## [0.9.0](https://www.github.com/bihealth/varfish-server-worker/compare/v0.8.0...v0.9.0) (2023-07-05) ### Features * adding allelic balance for SVs ([#127](https://www.github.com/bihealth/varfish-server-worker/issues/127)) ([564a7ec](https://www.github.com/bihealth/varfish-server-worker/commit/564a7ec44754b461255a0a316ecd5ae59c66b002)) * allow filtering SVs based on effect on transcript ([#129](https://www.github.com/bihealth/varfish-server-worker/issues/129)) ([#134](https://www.github.com/bihealth/varfish-server-worker/issues/134)) ([1aab8c8](https://www.github.com/bihealth/varfish-server-worker/commit/1aab8c84af684c844c30dfd2a1cec72f0a3a2fc8)) ### Bug Fixes * dependabot config and updates ([#133](https://www.github.com/bihealth/varfish-server-worker/issues/133)) ([006e306](https://www.github.com/bihealth/varfish-server-worker/commit/006e3068500c3eb311cfa528e10bfbaf86046cb8)) * removing unused dependencies ([#124](https://www.github.com/bihealth/varfish-server-worker/issues/124)) ([2cee74b](https://www.github.com/bihealth/varfish-server-worker/commit/2cee74be09f97400ae3e59bc9a2bb435ff3956b2)) * specification of genomic range in query ([#126](https://www.github.com/bihealth/varfish-server-worker/issues/126)) ([6eddaef](https://www.github.com/bihealth/varfish-server-worker/commit/6eddaefc0b401d19755bd053ea79d09e31f4302a)) ## [0.8.0](https://www.github.com/bihealth/varfish-server-worker/compare/v0.7.0...v0.8.0) (2023-06-28) ### ⚠ BREAKING CHANGES * remove REST server related code (#122) (#123) * replace db-compile with per-output commands (#112) (#121) ### Code Refactoring * remove code that was moved to viguno/annonars ([#116](https://www.github.com/bihealth/varfish-server-worker/issues/116)) ([#117](https://www.github.com/bihealth/varfish-server-worker/issues/117)) ([50099dd](https://www.github.com/bihealth/varfish-server-worker/commit/50099dd01552f2b270728537ed34c01172de0e31)) * remove REST server related code ([#122](https://www.github.com/bihealth/varfish-server-worker/issues/122)) ([#123](https://www.github.com/bihealth/varfish-server-worker/issues/123)) ([0b68809](https://www.github.com/bihealth/varfish-server-worker/commit/0b68809275294dd295b72fc73faa8fc26c095723)) * replace db-compile with per-output commands ([#112](https://www.github.com/bihealth/varfish-server-worker/issues/112)) ([#121](https://www.github.com/bihealth/varfish-server-worker/issues/121)) ([5da2799](https://www.github.com/bihealth/varfish-server-worker/commit/5da27991765cdc294a4114aa57dbb2464e112d6e)) ## [0.7.0](https://www.github.com/bihealth/varfish-server-worker/compare/v0.6.1...v0.7.0) (2023-06-09) ### Features * add "db genes query" command ([#109](https://www.github.com/bihealth/varfish-server-worker/issues/109)) ([27e995c](https://www.github.com/bihealth/varfish-server-worker/commit/27e995c9a1127f2e2fc41a5481b2ae07a3518ea7)) * adding "pheno prune" command against all-parents annotation ([#100](https://www.github.com/bihealth/varfish-server-worker/issues/100)) ([#114](https://www.github.com/bihealth/varfish-server-worker/issues/114)) ([c77b2d4](https://www.github.com/bihealth/varfish-server-worker/commit/c77b2d4dbd2a3708368fccc1371b2f6364042440)) * adding genes database ([#85](https://www.github.com/bihealth/varfish-server-worker/issues/85)) ([#90](https://www.github.com/bihealth/varfish-server-worker/issues/90)) ([634e281](https://www.github.com/bihealth/varfish-server-worker/commit/634e281c2528f3a6b072e36618509faa74c796e7)) * adding sequence variant databases ([#94](https://www.github.com/bihealth/varfish-server-worker/issues/94)) ([74f985a](https://www.github.com/bihealth/varfish-server-worker/commit/74f985ae6ba945d2cda1c4d5ceab277d309ba675)) * individual paths for "db genes build" ([#106](https://www.github.com/bihealth/varfish-server-worker/issues/106)) ([0a10a4e](https://www.github.com/bihealth/varfish-server-worker/commit/0a10a4e0f93129fe01cb9df77b80272a9652dc23)) * move from flatbuffers to protocol buffers ([#89](https://www.github.com/bihealth/varfish-server-worker/issues/89)) ([#99](https://www.github.com/bihealth/varfish-server-worker/issues/99)) ([cff7ace](https://www.github.com/bihealth/varfish-server-worker/commit/cff7ace317d705fe46fa106ea3a56a1fe9b34457)) * support for dbNSFP gene information ([#97](https://www.github.com/bihealth/varfish-server-worker/issues/97)) ([#102](https://www.github.com/bihealth/varfish-server-worker/issues/102)) ([0448bcb](https://www.github.com/bihealth/varfish-server-worker/commit/0448bcba3e39eca1d69c3553d711feba9e275b46)) * use protobuf/prost for gene information storage ([#96](https://www.github.com/bihealth/varfish-server-worker/issues/96)) ([#101](https://www.github.com/bihealth/varfish-server-worker/issues/101)) ([6a97fb6](https://www.github.com/bihealth/varfish-server-worker/commit/6a97fb6c58c9800c519969c99b0373b915420e72)) ### [0.6.1](https://www.github.com/bihealth/varfish-server-worker/compare/v0.6.0...v0.6.1) (2023-05-03) ### Bug Fixes * "db mk-inhouse" command for breakends ([#79](https://www.github.com/bihealth/varfish-server-worker/issues/79)) ([9b33e1d](https://www.github.com/bihealth/varfish-server-worker/commit/9b33e1d31cdbef31c636da40d1394eac63fb322f)) * command "sv query" for types BND and INS ([#81](https://www.github.com/bihealth/varfish-server-worker/issues/81)) ([5be2274](https://www.github.com/bihealth/varfish-server-worker/commit/5be2274c86f86f3ae32b255f3e778ddebc1c7a28)) * correctly interpret "callers" column ([#82](https://www.github.com/bihealth/varfish-server-worker/issues/82)) ([8e083c8](https://www.github.com/bihealth/varfish-server-worker/commit/8e083c87b3d5e7d263ade2d4540f06250b20bc6b)) * overlap queries for BND and INS ([#83](https://www.github.com/bihealth/varfish-server-worker/issues/83)) ([4de4eda](https://www.github.com/bihealth/varfish-server-worker/commit/4de4eda55c2caa34881305339a194eae2125b2f1)) ## [0.6.0](https://www.github.com/bihealth/varfish-server-worker/compare/v0.5.1...v0.6.0) (2023-05-02) ### Features * add "serve pheno" REST API service ([#72](https://www.github.com/bihealth/varfish-server-worker/issues/72)) ([#73](https://www.github.com/bihealth/varfish-server-worker/issues/73)) ([17c9dd5](https://www.github.com/bihealth/varfish-server-worker/commit/17c9dd53c0a14949087e03b840dd0e7f50a1b55e)) ### [0.5.1](https://www.github.com/bihealth/varfish-server-worker/compare/v0.5.0...v0.5.1) (2023-03-14) ### Bug Fixes * reciprocal overlap computation ([#69](https://www.github.com/bihealth/varfish-server-worker/issues/69)) ([6165d9f](https://www.github.com/bihealth/varfish-server-worker/commit/6165d9f4f8df412ccb5bfbd6a8d4783f6f3d0e15)) * region deserialization in sv query ([#70](https://www.github.com/bihealth/varfish-server-worker/issues/70)) ([7a577e3](https://www.github.com/bihealth/varfish-server-worker/commit/7a577e3f5f2711f0247e6fc0e7f332af450e1197)) ## [0.5.0](https://www.github.com/bihealth/varfish-server-worker/compare/v0.4.0...v0.5.0) (2023-02-13) ### Features * annotate SVs with masked sequence overlap ([#63](https://www.github.com/bihealth/varfish-server-worker/issues/63)) ([#66](https://www.github.com/bihealth/varfish-server-worker/issues/66)) ([0fd9403](https://www.github.com/bihealth/varfish-server-worker/commit/0fd940362f820913a71fbca5c53194206e097792)) * implement gene allow lists for "sv query" ([#65](https://www.github.com/bihealth/varfish-server-worker/issues/65)) ([#67](https://www.github.com/bihealth/varfish-server-worker/issues/67)) ([aa9da21](https://www.github.com/bihealth/varfish-server-worker/commit/aa9da21b27a0ba30b8a2589f543a44643815abc2)) * serve genome browser tracks from database ([#59](https://www.github.com/bihealth/varfish-server-worker/issues/59)) ([#60](https://www.github.com/bihealth/varfish-server-worker/issues/60)) ([040c522](https://www.github.com/bihealth/varfish-server-worker/commit/040c5227b251d76594acfa93f714305e0910eca5)) * write out effective and matched genotype from rules ([#64](https://www.github.com/bihealth/varfish-server-worker/issues/64)) ([#68](https://www.github.com/bihealth/varfish-server-worker/issues/68)) ([2c2c793](https://www.github.com/bihealth/varfish-server-worker/commit/2c2c7934d3fe333d72b709847a1c4c4a48375973)) ### Bug Fixes * hgnc xlink path ([#62](https://www.github.com/bihealth/varfish-server-worker/issues/62)) ([985cc33](https://www.github.com/bihealth/varfish-server-worker/commit/985cc334e99e6d693c3a665b34a825d28f4c81b6)) ## [0.4.0](https://www.github.com/bihealth/varfish-server-worker/compare/v0.3.0...v0.4.0) (2023-02-09) ### Features * add "server rest" sub command ([#57](https://www.github.com/bihealth/varfish-server-worker/issues/57)) ([#58](https://www.github.com/bihealth/varfish-server-worker/issues/58)) ([4b41010](https://www.github.com/bihealth/varfish-server-worker/commit/4b41010fb4acddf18f44904358d61a21dcfe8df6)) * implement "db compile" sub command ([#54](https://www.github.com/bihealth/varfish-server-worker/issues/54)) ([#55](https://www.github.com/bihealth/varfish-server-worker/issues/55)) ([7aa8c69](https://www.github.com/bihealth/varfish-server-worker/commit/7aa8c692bcef4d39c7b8aa6b82be5a5087ea8658)) ## [0.3.0](https://www.github.com/bihealth/varfish-server-worker/compare/v0.2.1...v0.3.0) (2023-02-01) ### ⚠ BREAKING CHANGES * enums serialization case and query issues (#41) ### Features * allow configuring whether missing call_info entry is pass ([#47](https://www.github.com/bihealth/varfish-server-worker/issues/47)) ([#49](https://www.github.com/bihealth/varfish-server-worker/issues/49)) ([4d0f64d](https://www.github.com/bihealth/varfish-server-worker/commit/4d0f64da21eb883cd7c31d56c9eacddd9fb4361b)) * make clinvar/pathogenic SV overlap configurable ([#39](https://www.github.com/bihealth/varfish-server-worker/issues/39)) ([af36bd4](https://www.github.com/bihealth/varfish-server-worker/commit/af36bd47dc50740543b6125e555aad7fe25e81e4)) * make TAD set configurable in query ([#51](https://www.github.com/bihealth/varfish-server-worker/issues/51)) ([82d4995](https://www.github.com/bihealth/varfish-server-worker/commit/82d4995ca727e46018a30520da48b31d774b7e23)) * removing minimal overlap for pathogenic variants again ([#53](https://www.github.com/bihealth/varfish-server-worker/issues/53)) ([3a5d427](https://www.github.com/bihealth/varfish-server-worker/commit/3a5d427ac3e6feaac74ee555752b56faf04ffd27)) * write out bg db overlap counts in "sv query" ([#44](https://www.github.com/bihealth/varfish-server-worker/issues/44)) ([#46](https://www.github.com/bihealth/varfish-server-worker/issues/46)) ([7286d0d](https://www.github.com/bihealth/varfish-server-worker/commit/7286d0d52d51eae39145772f9121f4c960f3fdd2)) * write out distance to next TAD boundary ([#45](https://www.github.com/bihealth/varfish-server-worker/issues/45)) ([#50](https://www.github.com/bihealth/varfish-server-worker/issues/50)) ([5ef72f3](https://www.github.com/bihealth/varfish-server-worker/commit/5ef72f32436c3e7d2116a26193935c7ed0db7b5a)) * writing out payload.sv_length ([#43](https://www.github.com/bihealth/varfish-server-worker/issues/43)) ([368621d](https://www.github.com/bihealth/varfish-server-worker/commit/368621dfbebfb1e0b1c1eb40f466277780cca82e)) ### Bug Fixes * enums serialization case and query issues ([#41](https://www.github.com/bihealth/varfish-server-worker/issues/41)) ([7cd73aa](https://www.github.com/bihealth/varfish-server-worker/commit/7cd73aae69421998500571decd9417f026824135)) ### Miscellaneous Chores * set next 0.3.0 ([101615d](https://www.github.com/bihealth/varfish-server-worker/commit/101615dbdaf3c302b226aaaec77866ba31aca5ae)) ### [0.2.1](https://www.github.com/bihealth/varfish-server-worker/compare/v0.2.0...v0.2.1) (2023-01-31) ### Bug Fixes * pinning flatc-rust ([#37](https://www.github.com/bihealth/varfish-server-worker/issues/37)) ([e9d1d89](https://www.github.com/bihealth/varfish-server-worker/commit/e9d1d89a16fe5c962cfe97e215f378ba138968e4)) ## [0.2.0](https://www.github.com/bihealth/varfish-server-worker/compare/v0.1.0...v0.2.0) (2023-01-31) ### Features * adding --max-results for "sv query" sub command ([#32](https://www.github.com/bihealth/varfish-server-worker/issues/32)) ([#33](https://www.github.com/bihealth/varfish-server-worker/issues/33)) ([4aa7094](https://www.github.com/bihealth/varfish-server-worker/commit/4aa709468d0e8a3bdd3aaa78b6376b9a31f08c25)) * annotate ACMG and OMIM genes in "sv query" ([#31](https://www.github.com/bihealth/varfish-server-worker/issues/31)) ([#35](https://www.github.com/bihealth/varfish-server-worker/issues/35)) ([9058e2a](https://www.github.com/bihealth/varfish-server-worker/commit/9058e2aca09e97e908009af7f00c3e6663a73ee6)) ## 0.1.0 (2023-01-30) ### Features * "sv query" now writes out TSV with information for a MVP ([#28](https://www.github.com/bihealth/varfish-server-worker/issues/28)) ([6a928c8](https://www.github.com/bihealth/varfish-server-worker/commit/6a928c8d92d136bc5f53d8204aae3da85815c07f)) * add "sv build-bgdb" command ([#18](https://www.github.com/bihealth/varfish-server-worker/issues/18)) ([#19](https://www.github.com/bihealth/varfish-server-worker/issues/19)) ([00cdf41](https://www.github.com/bihealth/varfish-server-worker/commit/00cdf413ddd9b18994a8ba4f0e4902aa37adbaa1)) * annotating SVs with ClinVar VCV ([#27](https://www.github.com/bihealth/varfish-server-worker/issues/27)) ([14af2bc](https://www.github.com/bihealth/varfish-server-worker/commit/14af2bc7c41126a43639fd75b4a277bf2c8ceddd)) * bootstrapping sv-query sub command ([#2](https://www.github.com/bihealth/varfish-server-worker/issues/2)) ([9cb0c95](https://www.github.com/bihealth/varfish-server-worker/commit/9cb0c95a390a99293bee6862ef80efc3b9437429)) * implement proper counting of background records ([#13](https://www.github.com/bihealth/varfish-server-worker/issues/13)) ([#14](https://www.github.com/bihealth/varfish-server-worker/issues/14)) ([a0965cc](https://www.github.com/bihealth/varfish-server-worker/commit/a0965cc1eeb5c73c6becc9f7c1d62f4d12030093)) * implement public/in-house SV database interval tree construction ([#4](https://www.github.com/bihealth/varfish-server-worker/issues/4)) ([#5](https://www.github.com/bihealth/varfish-server-worker/issues/5)) ([03442aa](https://www.github.com/bihealth/varfish-server-worker/commit/03442aa89769a12eb75fbad01d791bb9e29e5445)) * implement query schemas (10) ([#11](https://www.github.com/bihealth/varfish-server-worker/issues/11)) ([cc087d7](https://www.github.com/bihealth/varfish-server-worker/commit/cc087d7d8198d901feb97745f18627efcc391c3c)) * implementing PoC query feature with SV VCF ([#6](https://www.github.com/bihealth/varfish-server-worker/issues/6)) ([#7](https://www.github.com/bihealth/varfish-server-worker/issues/7)) ([925ebd8](https://www.github.com/bihealth/varfish-server-worker/commit/925ebd85bf8d50d9debd6a5dca9e8851bc90955a)) * make "sv query-next" feature-complete for a MVP ([#24](https://www.github.com/bihealth/varfish-server-worker/issues/24)) ([#25](https://www.github.com/bihealth/varfish-server-worker/issues/25)) ([b7c873c](https://www.github.com/bihealth/varfish-server-worker/commit/b7c873c3f46c8bb393a26407037fe9f90995ec63)) * PoC implementation of variant filtration ([#15](https://www.github.com/bihealth/varfish-server-worker/issues/15)) ([#16](https://www.github.com/bihealth/varfish-server-worker/issues/16)) ([12201ca](https://www.github.com/bihealth/varfish-server-worker/commit/12201ca6f3ad1db7564252ffa905fc438895d3c0)) * read query from JSON file ([#22](https://www.github.com/bihealth/varfish-server-worker/issues/22)) ([#23](https://www.github.com/bihealth/varfish-server-worker/issues/23)) ([4e41fbc](https://www.github.com/bihealth/varfish-server-worker/commit/4e41fbc72eff9f25d7cd59b714c89a369e204eb4)) * switching CLI to multiple sub command levels ([#17](https://www.github.com/bihealth/varfish-server-worker/issues/17)) ([9af47df](https://www.github.com/bihealth/varfish-server-worker/commit/9af47dfc358b70a9fcf7e5bcb50a1e2b14e4fa0c)) * using reasonble settings for sv query poc ([#20](https://www.github.com/bihealth/varfish-server-worker/issues/20)) ([#21](https://www.github.com/bihealth/varfish-server-worker/issues/21)) ([26c0ba0](https://www.github.com/bihealth/varfish-server-worker/commit/26c0ba021d21d0969cfc68806a136060902c273b)) ### Performance Improvements * adjust interval types ([#6](https://www.github.com/bihealth/varfish-server-worker/issues/6)) ([#9](https://www.github.com/bihealth/varfish-server-worker/issues/9)) ([76d254b](https://www.github.com/bihealth/varfish-server-worker/commit/76d254be54b499455a1e02d0bde6af08aea9913f))