# Changelog ### [1.7.9](https://www.github.com/orthanq/orthanq/compare/v1.7.8...v1.7.9) (2024-10-07) ### Bug Fixes * remove if-else block from the linear interpolation func ([#35](https://www.github.com/orthanq/orthanq/issues/35)) ([d0b4562](https://www.github.com/orthanq/orthanq/commit/d0b4562049ecc1458b0e75f5914d239572610a70)) ### [1.7.8](https://www.github.com/orthanq/orthanq/compare/v1.7.7...v1.7.8) (2024-08-24) ### Bug Fixes * handle allele name parsing from xml with and without HLA prefix ([#33](https://www.github.com/orthanq/orthanq/issues/33)) ([9bcf1f9](https://www.github.com/orthanq/orthanq/commit/9bcf1f9d271ff6cbc151b51163081d30b31b434a)) ### [1.7.7](https://www.github.com/orthanq/orthanq/compare/v1.7.6...v1.7.7) (2024-08-23) ### Bug Fixes * fix threshold for considered variants to long argument and lower threshold ([#31](https://www.github.com/orthanq/orthanq/issues/31)) ([6062f8a](https://www.github.com/orthanq/orthanq/commit/6062f8a58b7e9ccaab1e1c9ff76c9a36147e6eed)) ### [1.7.6](https://www.github.com/orthanq/orthanq/compare/v1.7.5...v1.7.6) (2024-08-22) ### Bug Fixes * fix equivalence class generation for hla and virus case separately; further, implement a flag for extension of haplotype list after linear program computation ([#29](https://www.github.com/orthanq/orthanq/issues/29)) ([cc7a92d](https://www.github.com/orthanq/orthanq/commit/cc7a92df98e6f04cb63d5bf6ac68914644792772)) ### [1.7.5](https://www.github.com/orthanq/orthanq/compare/v1.7.4...v1.7.5) (2024-08-19) ### Bug Fixes * implement user defined parameters threshold for equivalence classes and extending haplotype list; also properly adjust path of equivalence class graph ([#27](https://www.github.com/orthanq/orthanq/issues/27)) ([b9f8255](https://www.github.com/orthanq/orthanq/commit/b9f8255818360b16c76abaa41bc20e326a01f2c6)) ### [1.7.4](https://www.github.com/orthanq/orthanq/compare/v1.7.3...v1.7.4) (2024-08-15) ### Bug Fixes * fixate good_lp version and do not use wildcard constraint in cargo.toml ([68afd30](https://www.github.com/orthanq/orthanq/commit/68afd305236f85893fe68cec135c79d2ef19e983)) * fix scenario path for hla preprocessing ### [1.7.3](https://www.github.com/orthanq/orthanq/compare/v1.7.2...v1.7.3) (2024-08-14) ### Bug Fixes * add description and license info to cargo.toml ([#23](https://www.github.com/orthanq/orthanq/issues/23)) ([a3036e9](https://www.github.com/orthanq/orthanq/commit/a3036e9b265c164fccc3ef1abd672de3feefe2e2)) * fix no such file or directory error by reading scenario to string and writing it to a temp. ### [1.7.2](https://www.github.com/orthanq/orthanq/compare/v1.7.1...v1.7.2) (2024-08-14) ### Bug Fixes * perform interpolation of allele frequency distribution on the probability scale instead of PHRED scale; further, this changes AF distribution display to a bubble chart ([#21](https://www.github.com/orthanq/orthanq/issues/21)) ([309d33a](https://www.github.com/orthanq/orthanq/commit/309d33a9f2517b9e6362e693b666dedb667e4407)) ### [1.7.1](https://www.github.com/orthanq/orthanq/compare/v1.7.0...v1.7.1) (2024-08-05) ### Bug Fixes * fix preprocess hla outputs ([#19](https://www.github.com/orthanq/orthanq/issues/19)) ([34c78ae](https://www.github.com/orthanq/orthanq/commit/34c78aebfcdd7b77b2eb9d1a051ee45cb51e2dcd)) ## [1.7.0](https://www.github.com/orthanq/orthanq/compare/v1.6.0...v1.7.0) (2024-07-17) ### Features * implement generic virus application ([#17](https://www.github.com/orthanq/orthanq/issues/17)) ([05bfe4e](https://www.github.com/orthanq/orthanq/commit/05bfe4e1f1efc90247da2db1d94e9e5b60326925)) ## [1.6.0](https://www.github.com/orthanq/orthanq/compare/v1.5.0...v1.6.0) (2024-07-08) ### Features * set a configurable threshold that data has sufficient observation ([#15](https://www.github.com/orthanq/orthanq/issues/15)) ([09bea42](https://www.github.com/orthanq/orthanq/commit/09bea426a813e1231380a030115710b318f7a048)) ## [1.5.0](https://www.github.com/orthanq/orthanq/compare/v1.4.0...v1.5.0) (2024-06-25) ### Features * optimize model by pruning search space ([#8](https://www.github.com/orthanq/orthanq/issues/8)) ([d16cbe8](https://www.github.com/orthanq/orthanq/commit/d16cbe853f61e1ec9e517632a7453aae42f5ab97)) ## [1.4.0](https://www.github.com/orthanq/orthanq/compare/v1.3.0...v1.4.0) (2024-06-20) ### Features * download nextstrain resources and generate candidate variants from nuc conversions ([#12](https://www.github.com/orthanq/orthanq/issues/12)) ([f1ffda9](https://www.github.com/orthanq/orthanq/commit/f1ffda92f328d4078746b0b374b9e9dc93f8037e)) ## [1.3.0](https://www.github.com/orthanq/orthanq/compare/v1.2.0...v1.3.0) (2024-04-12) ### Features * breaking change: orthanq virus candidates: use the oldest submitted genome to represent each nextstrain in candidate haplotypes avoiding irrelevant pango lineages ([96f397b](https://www.github.com/orthanq/orthanq/commit/96f397b0ba99f0f695b93b75303da3ed0d269b52)) ## [1.2.0](https://www.github.com/orthanq/orthanq/compare/v1.1.0...v1.2.0) (2024-02-05) ### Features * retrieve metadata and download data packages belonging to sarscov2 and use in candidate variant generation ([#6](https://www.github.com/orthanq/orthanq/issues/6)) ([dfce2a5](https://www.github.com/orthanq/orthanq/commit/dfce2a57d257e075765230b16cbaac1cd6d00ae7)) ## [1.1.0](https://www.github.com/orthanq/orthanq/compare/v1.0.1...v1.1.0) (2024-01-05) ### Features * enable viral quantification ([#4](https://www.github.com/orthanq/orthanq/issues/4)) ([b945239](https://www.github.com/orthanq/orthanq/commit/b945239b81293f6520ad7cb0def6cbb235dca517)) ### [1.0.1](https://www.github.com/orthanq/orthanq/compare/v1.0.0...v1.0.1) (2023-12-21) ### Miscellaneous Chores * release 1.0.1 ([af15015](https://www.github.com/orthanq/orthanq/commit/af15015df8b83c89c74ab571d2dd61582355c980)) ## 1.0.0 (2023-12-21) ### Features * output 2-field info by summing up densitites of events that have identical first two fields ([dbd192c](https://www.github.com/orthanq/orthanq/commit/dbd192c3349deda41938d346028b3cfd617f8d40)) ### Miscellaneous Chores * release 1.0.0 ([827179b](https://www.github.com/orthanq/orthanq/commit/827179b814ce0246e4d72c2eb47da3fadbd402ee))