2.15.3 (2024-08-28)
- data: track singular variants (fb1ebbd)
- data: update data (c8100ec)
- namedallelematcher: fix permutation generation with mix of phased/unphased data (2146db0)
- phenotyper: improve support for combinations in outside calls (b1a6deb)
- reporter: fix limiting reports by source (ac0c52e)
- reporter: fix matching diplotype-specific recommendations (11fc7b4)
- reporter: take subsetting into account when calculating total genes (6ef47cc)
2.15.2 (2024-08-20)
- data: fill in DPYD lookupkeys for DPWG (90d587b)
- tools: gene regions for F5, CYP2D6, VKORC1, IFNL4 for research purposes (5f0e6dd)
- tools: show the name of the sample whose result files are being processed (8d6d1c8)
2.15.1 (2024-08-17)
- do not require any base filename before the sample IDs (7250db4)
- validate outside call diplotypes (9c49fbc)
- data: include missing CPIC metoprolol guidance (b117835)
- subsetter: fix bugs in subsetter (683a361)
2.15.0 (2024-08-06)
- json2tsv: report error when no allele definition json can be found (03a8b1f)
- phenotyper: generate diplotype data (ed4d03f)
- fix haplotype name sorting (f9888b0)
- improve Subsetter (971ba16)
- reduce data size (5bdcc49)
- data: update data (a57b955)
- json2tsv: allow the script to find the allele definition jsons from wherever it is run (03151ba)
- namedallelematcher: avoid exceptions (f4fe35a)
- namedallelematcher: fix handling of phased DPYD HapB3 alleles (286b76d)
- namedallelematcher: make NamedAllele.structuralVariant a private property (df68105)
- namedallelematcher: make sure cached properties are updated correctly (ab1e194)
- phenotyper: fix typo in CYP2D6 activity value assignment and drug count (36cc688)
- phenotyper: fix typo in two specific CYP2D6 diplotype activity score assignment (cae0f8c)
- phenotyper: use correct comparator (4cf8cb2)
- preprocessor: resolve errors caused by similar sample names (905b2c3)
- subsetter: fix how numeric cells are handled in Excel (bbaa135)
2.14.0 (2024-07-19)
- data: make all allele definitions import from PharmGKB (47da939)
- data: update to PharmVar v6.1.3 (e4b8fc2)
- data: fix downloading new guidance data (a1007c0)
- diplotype-comparator: update string delimiter (e10a2ea)
- namedallelematcher: fix exception thrown while sorting diplotype matches (093f5b2)
- namedallelematcher: handle CYP2D6 and HLA outside calls with sub-alleles gracefully (dcaa055)
- reporter: fix how allele presence phenotypes are shown in final report (2f00c6c)
- reporter: fix missing PMID in report citation data (81a0df2), closes #187
- reporter: fix multiple version check logic (3af2726)
- reporter: fix phenotype check by querying only phenotype-related genes in an annotation (b666953), closes #180
- reporter: warn if multiple versions found (9bb2a55)
2.13.0 (2024-06-11)
- diplotype-comparator: find equivalent phased alleles (a8a786c)
- pharmcat: add FDA drug guidance (ae6ea63)
- preprocessor: retain genomic regions specified in a bed file (d017be5)
- remove non-existent test class (1a91885)
- data: delete obsolete files before exporting positions (8acb549)
- datamanager: add support for subsetting allele definitions (79fb6ea)
- datamanager: handle all allele/position removal during data ingestion phase (85a770f)
- datamanager: remove populationFrequency from named allele (never used) (5ecaa74)
- preprocessor: ploidy at multiallelic positions (8805275)
- preprocessor: ploidy in X chromosomes for -0/--missing-to-ref (9f83767)
2.12.0 (2024-4-23)
- pharmcat: support more than one outside call file (154ac49)
- pipeline: add the feature of bypassing the gVCF check to the pipeline (d38005e)
- add json2tsv script (dfabdc1)
- namedallelematcher: improve VCF warnings (1659e21)
- pharmcat: add to path in docker container to fix running scripts (57a956b)
- phenotyper: strip gene symbol prefix from outside call diplotype alleles (940f6cf)
- reporter: add "Activity Value" prefix to formatted function (8735554)
- reporter: avoid exception for multiple phenotypes or activity scores for warfarin (da65834), closes #180
- reporter: fix display of function/activity in variant position section (2181f31)
- reporter: no tags for CPIC warfarin report (3842c1f)
2.11.0 (2024-3-26)
- data: remove F5 (0c6123b)
- datamanager: make sure we remove obsolete data files (da21f6e)
2.10.0 (2024-3-25)
- 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
- 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)
- diplotype-comparator: reduce runtime (d17ca4a)
- revert message annotation update (6cf0e3b)
2.9.0 (2024-1-17)
- 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)
- 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
- improve runtime of diplotype comparison (406930c)
2.8.3 (2023-10-24)
- 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
2.8.2 (2023-10-02)
- data: update to PharmVar 6.0.7 (34e253b)
- namedallelematcher: fix ArrayIndexOutOfBoundsException bug (a29420a), closes #156
- phenotyper: consistently sort GenePhenotype.diplotypes (36f1aa5)
2.8.1 (2023-09-29)
- improve error handling in batch mode (b7c9e66)
- data: add more data validation (0388049)
- namedallelematcher: fix DPYD HapB3 phasing issue (256ac64), closes #155
2.8.0 (2023-09-22)
- 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)
2.7.1 (2023-09-09)
2.7.0 (2023-09-02)
- pharmcat: Use PharmGKB for all drug and phenotype annotations (7390fa1)
- reporter: add new footnote about CPIC/DPWG function (b986a13)
- 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)
2.6.0 (2023-08-08)
- data: update data to sync with CPIC 1.28 and latest PharmGKB (4cdfc34)
- 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)
2.5.0 (2023-06-12)
- namedallelematcher: support treating undocumented variation as reference (f5a5baa)
- 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)
2.4.0 (2023-05-01)
- update to yarn 3.5
- update data for CPIC and PharmVar content (8fe4173)
- update to latest CPIC/PharmVar data for CYP2D6 and SSRI/SNRIs (ebaea81)
- improve how DefinitionReader is instantiated (8596063)
- standardize output order (df675c2)
- data: update messages (2a371dc)
- data: update messages (1b4dd8b)
- namedallelematcher: do not expose novelAllele (cc93ed0)
- namedallelematcher: fix null in toString (cbf827a)
- namedallelematcher: track novel alleles for sample and fix erroneous novel allele error when novel allele occurs in different sample (b079c54)
- report: remove max-width from print style (d5909e0), closes #129
- reporter: handle missing gene report (f9d7dba)
- reporter: show gene in section 3 if uncallable but has data (264cb0e)
- update to yarn 3.5 (7d0eeb1)
2.3.0 (2023-03-14)
- bad link on homepage (03c788d), closes #127
- update data (c526cfc)
- update data (209032d)
- namedallelematcher: improve error message when invalid GT allele value is provided in VCF (4af5de0)
- pipeline: support specifying max java heap size for pipeline (bdea14f)
- reporter: wrap long calls nicely (9bc9cfb), closes #130
2.2.3 (2023-02-06)
- fix permissions on executables (3385186)
- update to latest CPIC/PharmVar data (905306f)
- reporter: fix case for allele function names (90922b5)
2.2.2 (2023-02-01)
- update to latest data from PharmVar and CPIC (6ac3aeb), closes #126
- docker: sanitize ownership of reference FASTA files (2599f4e)
- pharmcat: add pharmcat_pipeline script (5c2fd85)
- pharmcat: fix max -cp recommendation (76295d0)
2.2.1 (2023-01-21)
- preprocessor: strip AN/AC info out of single sample output (8554572)
2.2.0 (2023-01-20)
- namedallelematcher: support multisample VCF (4790ac0)
- pharmcat: add concurrency support to pharmcat (eba4c4c)
- data: update data (77e5430)
- namedAlleleMatcher: fix handling of homozygous combinations (e13b587)
- namedallelematcher: fix handling of homozygous result for DPYD (ea127ea)
- namedallelematcher: fix parsing of AD field (b6b0d73)
- namedallelematcher: fix parsing of AD field (04326ef), closes #118
- namedallelematcher: fix preprocessed spelling (e7c4a65)
- namedallelematcher: haplotype name comparison (8e1f547), closes #119
- namedallelematcher: read VCF into memory if possible (e1bc46d)
- namedallelematcher: support vcf.gz and vcf.bgz (1710217)
- pharmcat: fix -def flag parsing (3407310)
- pharmcat: fix BatchPharmCAT problems (7c045ff)
- pharmcat: improve pipeline, carry sample id throughout (1a3b954)
- pharmcat: support specifying sample; sort data model to keep tests stable (05007e3)
- preprocessor: add java check, support tool paths via environment variables (a762127)
- preprocessor: change the way to determine positions without any called genotype (ea43698)
- preprocessor: fix bugs introduced by DPYD change (c748725)
- preprocessor: fix output filename handling (ec26f66)
- preprocessor: move gvcf check to beginning (c9d3837)
- preprocessor: output single VCF by default (2bf0c74)
- preprocessor: print out the tool version (9edc5ef)
- reporter: rename "generatedOn" property to "timestamp" (c241d01)
2.1.2 (2022-11-11)
- namedAlleleMatcher: add support for PCATxINDEL from preprocessor (bc04d5d)
- preprocessor: bug in determining indel (35e25cc)
- preprocessor: fix a bug related to missing genotypes (ff676c3)
- preprocessor: fix a bug with the unspecified ALT (88b94d2)
- preprocessor: fix error for indels (0bc0b74)
- preprocessor: fix pharmcat positions file lookup logic (9f2a77a)
2.1.1 (2022-11-09)
- preprocessor: add version info and improve docs (8d1d785)
- preprocessor: fix automatic version update (c3d5940)
2.1.0 (2022-11-09)
- preprocessor: major refactoring and support for concurrent mode (ce5c3e5)
- bug in reference genome sequence (6fc5550)
- data: update to CPIC 1.21.3 (61143e6)
- preprocessor: fix a bug for alt=<*> (c3b96c3)
- preprocessor: process regions concurrently (7c4f581)
- preprocessor: add support for concurrent mode (71855f2)
2.0.3 (2022-10-27)
2.0.2 (2022-10-26)
- errors in the names of sex and mitochondria chromosomes in the reference genome sequence (b5e1412), closes #116
- fix support for haploid genes (chrX, chrY, chrM) (dc8a43d)
- data: fix problem with chrX data preprocessor relies on (2d71671)
- data: update to latest CPIC data (4393cb3)
2.0.1 (2022-10-25)
- preprocessor: declare and concat list variables (d0899f0), closes #115
- preprocessor: fix a bug in bcftools and bgzip version checks that interrupts the VCF preprocessor (34f3f54), closes #116
- preprocessor: fix a bug that interrupts the VCF preprocessor (0ed6e22), closes #115
2.0.0 (2022-10-20)
- reporter: this introduces changes to the phenotyper and reporter JSON files that are not backwards-compatible.
- org.pharmgkb.pharmcat.PharmCAT is now the only command line tool. All arguments have been changed except for -vcf.
This change will only impact you if you specify anything other than -vcf or use anything other than the main PharmCAT program.
- The command line arguments to modules have been standardized to match the main PharmCAT program.
- NamedAlleleMatcher: -d renamed -na, -a renamed -ar
- Phenotyper: -o renamed -a
- Reporter: -o renamed -f
- namedallelematcher: The NamedAlleleMatcher will always assume reference. This is no longer a runtime option.
- PharmCAT now requires Java 17
- gate CYP2D6 calling behind research flag (12e4fdf)
- require Java 17 (5ca456e)
- update PharmCAT pipeline tool arguments (08e6e22)
- data: add definition for CYP2D6 (f0ab563)
- datamanager: add DPWG allele defintions including CYP3A4 (1842f32)
- datamanager: add DPWG file processing to the DataManager (58f7691)
- namedallelematcher: add support for combinations and partials, update version to 2.0 (d3a6065)
- namedallelematcher: removing assumeReference (864fea0)
- phenotyper: add activity data to diplotypes and haplotypes (ec12285)
- phenotyper: make sample VCF data take precedence over outside calls (dc8f585)
- phenotyper: support outside activity score (52cfe3c)
- phenotyper: switch to preferring outside call data over VCF data and update wording accordingly (a3451aa)
- reporter: add back comments and activity score to report (1f55f7c)
- reporter: add DPWG drug data (7a32257)
- reporter: add DPYD-specific allele matcher for use in unphased data (2678251)
- reporter: add messages for combo and cyp2d6 modes (9604086)
- reporter: Add new Genotype, GuidelineReport, and AnnotationGroup models for organizing multiple results (c468223)
- reporter: add source labels to gene and drug summary (c6bda14)
- reporter: enable DrugCollection and GeneDrugSummary to run independently (17c773d)
- reporter: fix genotype matching for DPWG guidelines (e66d8c0)
- reporter: group genotype, function, and phenotype in gene summary of HTML report (d885cf0)
- reporter: label inferred diplotype calls in the final report data (32c48dc)
- reporter: make least-function allele calling work for DPYD in the reporter (5820d80)
- reporter: more work to change to GuidelineReport for data tracking (bf2fc7e)
- reporter: move population into drug table row header and fix row styling (2f610d2)
- reporter: rename "CPIC" recommendations to "Prescribing" recommendations (9d10303)
- reporter: reorder implications and recommendations columns in final report (e7542a1)
- reporter: separate CPIC/DPWG reports (87e4bd2)
- reporter: split Reporter class into separate AbstractFormat classes and retain ReportContext (d2ebd53)
- reporter: switch DPWG guideline data source to individual files (bd0e180)
- reporter: update formatting of the HTML report (a65913c)
- website: add a make task to publish a prototype of the PharmCAT website (5b8383b)
- reporter: improve function display for DPYD combo genotypes (b8a29ef)
- normalize cli args (f754e50)
- revert to GRCh38.p13 (0b0eeda)
- standardize source/version info throughout pipeline (679842c)
- update DataManager (61fb5d1)
- update to GRCh38.p14 (8fe2728)
- update to most recent PharmVar/CPIC/DPWG (c689178)
- make command line flags more consistent (28b31fb)
- data: add support for G6PD (5790da6)
- data: remove "total activity score" in DPWG data (db3273e)
- data: update data (3898afe)
- data: update data (721f77a)
- data: update data (fe8c19a)
- data: update data (d378fc8)
- data: update data to latest CPIC/DPWG (5f2cedb)
- data: update messages (3780c7d)
- datamanager: fix exemptions for ignored positions/alleles (ee9a41e)
- datamanager: fix logic and use proper exit code on error (1ca34a0)
- datamanager: handle 429 error codes (28b4422)
- datamanager: improve -sdl handling (c72a2e8)
- datamanager: support HGVS-based positions in exemptions (584d552)
- docker: update samtools versions (2486315)
- namedallelematcher: add effectively phased property (397ad5c)
- namedallelematcher: add runtime metadata (d988a77)
- namedallelematcher: add wobble support (1200b1f)
- namedallelematcher: call haplotypes for DPYD if no exact (effectively phased) diplotype match (492be33)
- namedallelematcher: fix handling of DPYD Reference (aa4d095)
- namedallelematcher: fix hetero pair matching in combinations (9d45ee3)
- namedallelematcher: improve combination scoring and support off-reference partials (439b6ba)
- namedallelematcher: improve DPYD support (1adbec1)
- namedallelematcher: improve matcher html output (93e75df)
- namedallelematcher: properly report phased status (b774b59)
- namedallelematcher: sort variants by VCF position (7a2980a)
- namedallelematcher: update combination name style (730af57)
- namedallelematcher: when assuming reference, use reference for position if reference named allele has wobble (aca267e)
- pharmcat: add batch cli (f25fe58)
- pharmcat: cannot call System.exit or tests will fail (789da71)
- pharmcat: default to compact mode (6989be0)
- pharmcat: exit with proper exit codes (6b306b6)
- pharmcat: fix missing variant warnings when using serialized matcher data (ed34e28)
- pharmcat: maintain consistent base output file name (8ba7b6e), closes #113
- phenotyper: add support for calling CYP2D6 (aaa598a)
- phenotyper: allow diplotype and phenotype data in the outside calls (03dd114)
- phenotyper: avoid NPE when applying messages (fd07844)
- phenotyper: fix handling replacement of outside call for GeneReports in Phenotyper (c62d888)
- phenotyper: fix how DPYD phased alleles are reduced for lookup in Reporter (25493be)
- phenotyper: reorganize OutsideCall into phenotype package (5cbeb14)
- phenotyper: standardize GSON usage (79407e1)
- preprocessor: correct phasing status for multiallelic positions (59fb6b8), closes #102
- preprocessor: correct phasing status for multiallelic positions (52cc411), closes #102
- preprocessor: correct phasing status for multiallelic positions with mismatching alt (8bbb9a6), closes #102
- preprocessor: fix bug where VCF fields are not updated (af604db)
- preprocessor: harmonize arguments with PharmCAT (b98c8ef)
- preprocessor: keep the INFO/PX from refVcf in the output (7bb3d00)
- preprocessor: move bcftools and bgzip versions to global variables (3b4ffda)
- preprocessor: remove a line of test codes (24a5881)
- preprocessor: remove pre-existing .tbi index file (7dd8c45)
- preprocessor: revert the changes on .bgz which is not the default file extension of bgzip (5b8e39c)
- preprocessor: sort non-PGx variants by genomic positions to prevent sorting error (0b52234)
- preprocessor: update the default output suffix (dc80699)
- preprocessor: use .bgz as a bgzipped file extension for clarify (6b0e96f)
- preprocessor: use sample IDs as the default output prefix (b25b478)
- preprocessor: use the .bgz for bgzipped files (9df0fa5)
- preprocessor: warn and quit if a lower version of bcftools is used (49b3d29)
- reporter: add support for CPIC version (b6b4714)
- reporter: add validation for messages (530c88b)
- reporter: cleanup and use correct section name (cea8f15)
- reporter: cleanup api (87bf8c8)
- reporter: correctly fill CYP2D6 copy number diplotype (8d68b1e)
- reporter: don't store sample-specific info in DPWG data model (06c3ed9)
- reporter: extract TextConstants (fdf51bb)
- reporter: fix allele presence matching for DPWG guidelines (bdca135)
- reporter: fix bad references to ReportContext and DrugLink comparison (c89ca70)
- reporter: fix bug with calculating possible genotypes for DPWG guidelines (f0cc372)
- reporter: fix comparison of drug objects (7289b0c)
- reporter: fix duplication of drugs in gene summary (d53fe0b)
- reporter: fix function lookup when second allele is not present (872f690)
- reporter: fix HLA group names to work with phenotype comparison (3ab2356)
- reporter: fix unclosed HTML element in template (8b248ea)
- reporter: fix warfarin flowchart (204bef9)
- reporter: force background colors in print media (9d714bf)
- reporter: improve message handling to support source-specific messages and warfarin craziness (9744883)
- reporter: improve outside call handling (a580e32)
- reporter: make OutsideCallParser tolerate empty lines (78c1b36)
- reporter: more fixes for problems introduced with Diplotype refactor (300a775)
- reporter: more improvements and messaging tweaks (07781a3)
- reporter: move DpydCaller into reporter.caller package (8f7220e)
- reporter: move title, date, and version back into ReportContext (ebb4aa3)
- reporter: outside call now sets source diplotypes (e2bc62e)
- reporter: rename LeastFunctionUtils to DpydCaller (1dabc8e)
- reporter: render recommendation HTML properly (1145479)
- reporter: reorganize message handling (06c4056)
- reporter: reporter improvements (f418167)
- reporter: show drug annotations in the report again (e2daaf2)
- reporter: standardize GSON usage and use Env instead of using new DefinitionReader (31cf889)
- reporter: support inferring CYP2D6 copy number (1448764)
- reporter: update missing variant input display (9e0fe5a)
- reporter: use unicode GTE (84843e3)
- reporter: validate that PharmGKB annotations contain groups (43340f8)
- website: fix typos and broken links (5cdfc87)
- namedallelematcher: cache allele lookups (13731b2)
- pharmcat: skip reading/writing files if possible (37c0491)
1.8.0 (2022-05-06)
- update to latest PharmVar (5.1.14) data for CYP2C9 (2d9de55)
- fix VcfReaderTest for updated wording (870b3b9)
- data: update to CPIC 1.17.1 and PharmVar 5.1.14 (d205472)
- preprocessor: clarify the handling of mismatched VCF entries (b284637)
1.7.0 (2022-04-26)
- add a tracking event to the download button (04f2062)
- add umami analytics to the pharmcat.org site (82d8cd8)
- CYP2D6 code and documentation for StellarPGx (0b400ac)
- update to v1.17 of CPIC and v5.1.12 of PharmVar (0dcf2c9)
- preprocessor: handle alt=<*> for INDELs (776f32a)
- reporter: add a "test mode" to the Reporter (7799d91)
- reporter: add outside phenotype calls and support allele status genes (d528d7a)
- fix command line arg for supplying your own named alleles (4a8c84f)
- update site config (07d23cc)
- namedallelematcher: improve warnings about structural variations (63903df)
- preprocessor: handle alt=<*> (unspecific alleles) for SNPs (9c70001)
- reporter: fix handling of G6PD (cbcfb05)
- reporter: fix test outside call files for new syntax (39ed203)
- reporter: hide genes that are not reportable in the genotype table of the report (51a1bf7)
1.6.0 (2022-03-31)
- pharmcat.org website redesign and new content (48cd154)
- website: tweak the website styling and layout (b52b7d6)
- add more clarifying info to TestVcfBuilder alt allele mismatch message (63d0dfd)
- fix bundle call for running local jekyll (a1034a7)
- fix CLI arg description for Phenotyper (f31085c)
- fix jekyll front matter on disclaimers page (a2ecb79)
- fix permissions on VCF scripts (3d5cb34), closes #89
- data: update to CPIC 1.16 (5ee8d37)
- datamanager: correctly loading definitions in dataManager when skipping alleles (2687635)
- datamanager: improve error when encounter external service error (93de324)
- docker: make sure scripts are executable (dfc080f), closes #89
- docker: use docker 3.9 to work around numpy incompatibility (44cf6d1)
- namedallelematcher: discard position with AD field (6b717db)
- namedallelematcher: do not discard position if novel ALT allele is found (ba48472)
- namedallelematcher: handle
.AD value (2591ae9) - namedallelematcher: improve AD field handling (only catch reference overlap) (cb152c6)
- namedallelematcher: improve checking for unexpected ALT (f74b309)
- preprocessor: improved way to identify block gVCF (b57a6e2), closes #79
- preprocessor: sort VCF in a way that the non-PGx variants that occur at the PGx positions will appear after the line of the PGx variants (3a2be37), closes #95
- reporter: fix total gene count in report genotypes table (02fd57d)
- reporter: make DrugLinks comparable to sort properly in final output (501db22)
- reporter: update more PharmCATTest tests to new wrapper (89e5354)
- update TPMT test for new calling rules (63f4775)
1.5.1 (2022-02-22)
- data: add ABCG2 (92083db)
- reporter: hide gene in the genotype summary table if no data present (9db9de1)
1.5.0 (2022-02-19)
- reporter: show Matcher variant warnings in the final report (c247c99)
- preprocessor: flag non-PGx variants at PGx positions (908f6d9), closes #87
- data: update to CPIC 1.14 (e5ec432)
- namedallelematcher: add novel ALT warning (0ed4462)
- namedallelematcher: add support for PCATxALT and PCATxREF filters from preprocessor (a81e35c)
- preprocessor: reading of input file list and sample list (99d472c), closes #88
- preprocessor: remove key of chromosome positions only if the key is present in the dictionary (ebf5ac2)
- preprocessor: remove key of chromosome positions only if the key is present in the dictionary (0177a38)
- preprocessor: remove key only if the key is present in the dictionary (2f29fd1)
- preprocessor: remove PASS if the position is flagged for PharmCAT; update FILTER flag descriptions (f06c8c0)
1.4.0 (2022-01-28)
- datamanager: do not update docs if allele information not loaded (e5ca7ac)
- namedAlleleMatcher: warn if ref in definition does not match ref in VCF (e188e41)
- preprocessor: detect VCF samples that contains ',' which violates the VCF convention (59abc8a)
- preprocessor: homozygous reference at a single-nucleotide locus will not infer the genotype status of the INDELs at the same genomic position (261531b)
- preprocessor: improve annotations of ID and info columns (e0b8ba8)
- preprocessor: remove redundant homozygous reference check (bd8ba92)
1.3.1 (2022-01-14)
- data: CPIC update (097b275)
1.3.0 (2021-12-09)
- data: CPIC update (e741c7f)
- preprocessor: add missing multiallelic variants/positions as phased and bcftools determines phasing by GT delimiter accordingly (f7762ad), closes #78
- preprocessor: fix for PGx positions with missing ALT (e2592b2), closes #77
- preprocessor: fix output dir of a temp (f726303)
- preprocessor: interrupt and print a warning message if a gVCF input is detected (441a384)
1.2.1 (2021-11-18)
- data: fix bad genotype in a CYP2C19 test case (0a77c77)
- DataManager: support wobble code in reference allele (ada5a3a)
- DataManager: treat HGVS dup as a form of repeat [2] (81135db)
- preprocessor: fix vcf header parsing error (b5c9814)
1.2.0 (2021-10-27)
- remove UGT1A1 special handling and add more SLCO1B1 examples (74c9ae8)
- update vcf header and properly sort vcf after normalization (e512bc3)
- validate bgzip (78ccd71)
- data: update SLC01B1 data (47b572a)
- docker: update docker to use bgzipped reference FASTA (15e5977)
- docker: update docker to use bgzipped reference FASTA (9b594f6)
- NamedAlleleMatcher: improve warning message when GT in VCF doesn't have 2 alleles (890ae92)
- preprocessor: if output_folder is not specified, use parent directory of input (fef2722)
- preprocessor: improve how reference FASTA is obtained (9860ce2)
- preprocessor: update usage docs (0faf08e)
1.1.0 (2021-10-14)
- default '--ref_pgx_vcf' to 'pharmcat_positions.vcf.bgz' in the current working directory (eb34576)
- make output directory optional (55c244b), closes #68
- normalize "chrMT" to "chrM" (509c010)
- output dir of preprocessor now defaults to the dir of input VCF (c677e61)
- display version with --version flag (f7f6bbe)
- include URL to docs when multisample VCF is found (6105bcb)
- normalize "chrom" field to chrM for mitochondria (da2a456)
- remove pre-release note in PharmCAT runtime (81e9233)
- sort pharmcat_positions.vcf, add support for .bgz and .tbi of pharmcat_positions.vcf (2434f56)
- update processor details to v1.0.0 (ac3d001)
1.0.0 (2021-09-27)
- The allele definition format has been updated and is not backwards compatible.
- updating to Java 14
- add "pj" flag to PharmCAT class for writing Phenotyper output to a JSON file (5986b66)
- add a summary page to PharmCAT website (565f031)
- add AutogeneratedVcfTester (e504c24)
- add CLI option to get all results from NamedAlleleMatcher (40c4377)
- add CPIC version to Reporter output (83027f4)
- add docker support (b53f46d)
- add drugs file to DataManager and update drugs file (d604652)
- add exact-match-only to AutogeneratedVcfTester (fd14cd6)
- add messages to drug reports for certain gene calls (3da72a0)
- add option to PharmCAT runner to retain all scoring matches (f8b8ece)
- add support for MT-RNR1 (6d93598)
- add warning messages for ambiguous diplotype calls (2c2cc37)
- data update from CPIC and related changes (3d23a85)
- extract only exactly matched PGx variants (used to based on position) (e101d27)
- handle unassigned function alleles (cebfda9)
- make an explicit list of "reportable" drugs (99bf3b4)
- move CYP2D6 to list of preferred outside calls in summary report (8d07f60)
- new unphased data note in final report (826cbb5)
- normalize alleles for VCF (bfd37d8)
- option to keep intermediate files (882990b)
- option to provide a list of vcf files (dbef0c4)
- show matching diplotypes in final report recommendations sections (de18261)
- support new message annotation matching for ambiguous het calls (831fb79)
- take a file of samples to preprocess (b0f50f2)
- update report disclaimer template to match website (75d1af3)
- validate bcftools and tabix (252f7c1)
- add fuzzy match support to AutogeneratedVcfTester (296fef6)
- add overlap check to AutogeneratedVcfTester (bad7b98)
- ambiguous code expansion (f097ce7)
- ambiguous REF in output VCF files (d8a9c17)
- apply same criteria for ambiguity messages to genes and drugs (fa94e2a)
- change naming convention for IFNL3 to IFNL3/4 for final report (ffd1aa8)
- clean up message annotation matching (1c0b4f4)
- cleanup, appease linter (b260c24)
- custom definition transform for CYP2C19 *1 and *38 (1489005)
- default "No Result" value for uncalled genes when doing recommendation lookup (60961a8)
- default allHits/assumeReference in DefinitionExemption to be null (fcc23f2)
- download from url, test vcf (5840864)
- error in reading the sample file (9dccb85)
- exclude CYP2D6 from ExtractPositions (71ef0cb)
- file path split (62427e9)
- files containing wobble correctly identified (a561daf)
- finalize vcf query caching (b031691)
- fix ambiguity criteria for message annotation (2b0074e)
- fix bad import (4642716)
- fix COPY error in Dockerfile (37ddbfa)
- fix executable flag for test script (5274440)
- fix ExtractPositionsTest to also ignore genes (60d7e90)
- fix format of examples page on site (f8f4216)
- fix gradle "dataUpdate" task file paths to currently used paths (90e7372)
- fix missing variant column in genotype table of report (512742a)
- fix NPE when variant has no dbSNP ID (047313d)
- fix pre-release URL (a63e703)
- fix report layout (59b8e1c)
- fix sequence for deletion in NUDT15 definition (9a369d7)
- fix summary report of "outside call" genes and update summary page (a8e341c)
- fix the image URL for warfarin diagram (643317c)
- fix typo in message annotation data file (3b93329)
- fix warfarin display of recommendation text (57eaf10)
- fix wording for outside call alert (61419c9)
- fold pharmcat_positions.vcf into DataManager, remove pharmcat_intervals.txt (bf0caa5)
- generate uncompressed vcf (91bd1d2)
- handle ambiguous IUPAC codes properly (fef7251)
- handle long list of biobank samples (078f688)
- handle unexpected alleles gracefully (2dfbf0e)
- ignore MT-RNR1 on the reporter side (ed4ddb1)
- ignore positions with empty reference allele (b5198b0)
- import package (69ea88e)
- improve error message on reference allele mismatch, update positions_reference.tsv (e4f414d)
- indel ALT/REF and positions in output VCF (2f311e5)
- make gene section name consistent in final report (f8453ce)
- make het function phrases display consistently (d800c69)
- make Reporter follow the modular pattern (4b4f567)
- merge vcf position extraction and intervals into DataManager (ee7e70e)
- modify tabix error message (9a0fd2d)
- preprocessing test file format errors (b4234b1)
- prevent *1 from being shown as a relevent allele for all positions in CYP2C19 (57b8b27)
- print out the full error traceback message (a39b6c5)
- pull Sheets by URL instead of using Sheets API (5c1b482)
- remove "show-all-matches" option from PharmCAT class (062edec)
- remove cyvcf2 package that is not compatible with FIPS (37ec7e9)
- remove duplicate recommendations from Reporter output (0d319c5)
- remove references to unneeded pharmcat.properties file (66d726e)
- remove the import of cyvcf2 (62fc70c)
- remove unnecessary footnote from genotypes table in final report (191e469)
- restore default "assumeReference" behavior to UGT1A1 (8e871bb)
- show DiplotypeMatch names in order of haplotype names (83e31e5)
- show unphased footnote superscript on applicable calls (d28e181)
- support "." in VCF allele field (fbd20f0)
- support renaming downloaded fasta files (1c5ff92)
- support single allele call in VCF (988771b)
- switch named allele collection from List to SortedSet (c734716)
- take sorted by-chromosome VCFs as input (18a7fc9)
- test_gen scripts no longer need positions.vcf (d593d6e)
- update and fixes for allele definition data (ce11f6d)
- update copy for missing alleles in gene match section (4540cad)
- update CYP2C19 to account for new reference haplotype (e9856e1)
- update definitions (47c549f)
- update definitions/exemptions/messages (9a45d05)
- update shebang to use python3 (f103fd6)
- VCF filename matching with wobbles across runs (0b77cde)
- optimize log messages (a79ec99)
- updating to Java 14 (c91edeb)
0.8.0 (2021-03-31)
- add "label" field to Phenotyper output for diplotypes (b92b914)
- add new GenotypeInterpretation class (c90e358)
- add the reference flag to namedAllele objects (f02d872)
- add timer (eb5c997)
- add warfarin and peginterferon back in to drug list (18ed7f9)
- change gene-phenotype to use new layout (151de09)
- download to temp file (5c46985)
- enable Phenotyper to take either VCF input or NamedAlleleMatcher output JSON (1631d52), closes #39
- handle local files (9d0c46b)
- improve and expand outside call features (e2eedfc)
- include "comments" on recommendations in final report (71ce411)
- pull definitions from S3 and support ignored positions (4702f04)
- recursive output directory creation (b547294)
- reporter update intermediate check-in (33c560b)
- update gene definition files (141bed6)
- update to latest CPIC drugs and phenotypes (780a1f6)
- adjust TPMT variant count (dceb6ba)
- appease javadoc (6153145)
- avoid warning for transient Pattern in NamedAllele (4e27107)
- clear rsid map before rebuilding it (d9973b8)
- combine duplicate position columns from CYP2D6 translation (e70648d)
- display number of files produced (842414d)
- do not include data for anything involving blacklisted genes (408f503)
- DPYD chromosomal HGVS name (d82cb44)
- explicitly set date format (876182e)
- fix bug when diplotypes are specified in reverse order (fixes DPYD bug) (3849c47)
- fix bug when overriding callable genes with outside calls (85ad9f5)
- fix bugs and performance in ExtractPositions (95f3725), closes #34
- fix CFTR tests to remove F508del and change "Reference" (c50cfd4)
- fix CYP2C9 *2/*3 unit test (d82fd7e)
- fix delete obsolete files (11da562)
- fix DPYD integration test (524c3c3)
- fix gene definition files to make reference allele be first (0951f57)
- fix NamedAlleleMather tests to account for changed allele names (14f0f7f)
- fix recommendation matching for multi-gene guidelines (bd1ee0c)
- fix remove ignored positions not removing associated alleles (9ca4a2c), closes #36
- fix unsafe operation compiler warning (a081bb7)
- fix variant ordering bug (ee7e1af)
- fix VCF syntax for unspecified and deletion genotypes (5b6ae8e)
- improve handling of "Unknown" calls (a46866f)
- names for position chr6:18132163 in TPMT (39a99f7)
- remove "highlighted" drugs in final report (4a1f9ef)
- remove "no calls" from sample files (1fbb002)
- remove genes not used in recommendation match (7c027d9)
- remove ignored positions from named alleles as well (351979f)
- remove styling for Rx change in report (4e89125)
- remove tests for *60 UGT1A1 allele (80fbd5f)
- remove unnecessary variant allele options (f931b89)
- remove unused "g" option for PharmCAT CLI (f161a67)
- removed redundant convert_to_*.py scripts; condensed the scripts to one main script and one function library (8ef9f21)
- show genotype of "highlighted" variants in guideline section of report (f2bf726), closes #31
- skip import of allele definitions that have all alleles ignored (65dacd9)
- support ignored position exemptions (5ecb6e1)
- switch to PEP8 code style, clean up output, add basic input error checking (dac626c)
- take chr## or ## (-> chr##) for CHROM (9bce353)
- update input argument (2f57352)
- update test cases to adjust for changes to allele definitions and exemptions (cc0d997)
- speed up VCF preprocessing (d5a847d)