v2.10.0

2.10.0 (2024-3-25)

Features

• data: update to CPIC v1.38 and latest PharmVar (560bdb8)
• pharmcat: report RYR1 using lowest-function gene algorithm (596058a)
• preprocessor: an option to not perform a gVCF check (209f68f), closes #174

Bug Fixes

• data: update data (984c73a)
• namedallelematcher: update DPYD HapB3 support for HapB3 intronic allele (b32b4ae)
• preprocessor: improve message for gVCF (2d4da7d), closes #174
• reporter: add check for multiple conflicting phenotype/activity values (b9b1cd1)
• reporter: fix edge-case for outside calls of AS genes that only specify phenotype and not score (1321518)
• reporter: fix genotype display when no genotype is provided in outside call (1be5c6d)
• reporter: fix missing phenotype and activity score in drug section of HTML report (e3f1029)
• reporter: standardize naming (29e3900)

Performance Improvements

• diplotype-comparator: reduce runtime (d17ca4a)

Reverts

• revert message annotation update (6cf0e3b)

v2.9.0

2.9.0 (2024-1-17)

Features

• data: update to CPIC version v1.35 (5cb6717)
• data: update to PharmGKB version 2023-12-19 (66c49f9)
• reporter: add new "non-match" type of message (f5df05a)

Bug Fixes

• namedallelematcher: DPYD matching should ignore find-combinations mode (153853a)
• namedallelematcher: improve AD number warning (9d9a0b9), closes #168
• phenotyper: fix bug with stripping gene symbol from outside call diplotypes (cb97898), closes #161

Performance Improvements

• improve runtime of diplotype comparison (406930c)

v2.8.3

2.8.3 (2023-10-24)

This release supports Java 21.

Bug Fixes

• improve labeling of reference calls (4713b9b), closes #158
• data: fix date parsing for Java 21 (aba3dcd), closes #159
• reporter: fix version check for CPIC content (cb4b762), closes #157

v2.8.2

2.8.2 (2023-10-02)

Bug Fixes

• data: update to PharmVar 6.0.7 (34e253b)
• namedallelematcher: fix ArrayIndexOutOfBoundsException bug (a29420a), closes #156
• phenotyper: consistently sort GenePhenotype.diplotypes (36f1aa5)

v2.8.1

2.8.1 (2023-09-29)

This is a quick bug fix release for issue #155.

This release also renames the "Telti/Kobe" G6PD allele to "Telti, Kobe" to avoid confusion since diplotypes use "/" as a separator.

Bug Fixes

• improve error handling in batch mode (b7c9e66)
• data: add more data validation (0388049)
• namedallelematcher: fix DPYD HapB3 phasing issue (256ac64), closes #155

v2.8.0

2.8.0 (2023-09-22)

This release focuses on improving how PharmCAT calls DPYD's HapB3 allele and resolves #150.

Please consult the documentation as this will affect called diplotypes.

Features

• pharmcat: update DPYD matcher algorithm (763b950), closes #150

Bug Fixes

• pharmcat: allow reporter JSON in research mode (a3b0496)
• pharmcat: avoid NPE (a86daa6)
• pharmcat: avoid NPE (da11bd6)
• pharmcat: fix console message (f2b4086)
• pharmcat: fix how warnings are handled with outside calls (634f3b4), closes #154
• phenotyper: pass through outside calls even if no recommendations are available (03f7f7c), closes #154
• reporter: add DPYD warnings (2427813)

v2.7.1

2.7.1 (2023-09-09)

This is a quick data update.

We are aware of problems with calling DPYD and are actively working on it. To get updates on this, please see issue #150.

Bug Fixes

• data: revert removal of DPYD wobble handling (9a78c86)
• data: update to PharmVar 6.0.5 (63c717b)

v2.7.0

2.7.0 (2023-09-02)

Features

• pharmcat: Use PharmGKB for all drug and phenotype annotations (7390fa1)
• reporter: add new footnote about CPIC/DPWG function (b986a13)

Bug Fixes

• data: fix guideline citation data and update RYR1 phenotypes (93de1ff)
• pharmcat: disable reporter module when using research mode (d1b1822)
• preprocessor: capture both error and log from subprocess (c115ed2)
• preprocessor: install the scikit-allel that has a working toml file (77e2c43)

v2.6.0

2.6.0 (2023-08-08)

Features

• data: update data to sync with CPIC 1.28 and latest PharmGKB (4cdfc34)

Bug Fixes

• data: update data (76bfe08)
• data: update F5 version (43b6637)
• namedallelematcher: fix DPYD call with ref and partial (fa09226)
• namedallelematcher: improve DPYD calling (57b2bd8)
• namedallelematcher: improve DPYD calling with HapB3 wobble (3528815)
• namedallelematcher: support wobble in DPYD HapB3 (65a1309)
• namedallelematcher: update HTML output to use Bootstrap 5 (3774cca)
• pharmcat: fix NPE when called without -o flag (a8d5f51)
• preprocessor: pipe stdout to a user's running interface to show warning messages from a subprocess (36c151b)
• reporter: display allele function in section 3 (5f48358)
• reporter: don't emit empty ids (c7f3d48)
• reporter: fix browser upgrade CSS (6ba5bf1)
• reporter: fix links to uncallable genes in section 3 (f1d4da2)
• reporter: identify homozygous DPYD haplotypes (0f10fe3)
• reporter: improve allele match data for CYP2C19 *1 (2bc80cd)
• reporter: improve message for uncalled because of no data (8211015)
• reporter: improve text for uncallable genes (7e794b3)
• reporter: list function in section 3 (e51483c)
• reporter: show function in section 3 even when there is a no call (4e2ea20)
• reporter: show genes in section III if uncallable (7da2075)

v2.5.0

2.5.0 (2023-06-12)

Features

• namedallelematcher: support treating undocumented variation as reference (f5a5baa)

Bug Fixes

• fix loading of path for test file writing (beb03c3)
• data: update CPIC data (ab0fb0f)
• namedallelematcher: adhere to AD format rules (561012a), closes #139
• reporter: display consistent genotype in report, fix SLCO1B1 bug (08f65ea)
• reporter: fix DPWG version check (6c2d828)
• reporter: fix JSON property name (e7036c8)
• reporter: improve styling when there are multiple drug recommendations (20b20f4)