v1.3.0

1.3.0 (2021-12-09)

This update pulls in CPIC v1.11. It also includes a couple improvements to the preprocessor.

Features

• preprocessor: improve support for phased data, closes #75 #78

Bug Fixes

• data: update to CPIC v1.11 (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)

v1.2.1

1.2.1 (2021-11-18)

Bug Fixes

• 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)

v1.2.0

1.2.0 (2021-10-27)

This is mainly a data release.

Highlights:

• PharmCAT now bundles CPIC data v1.10.
• PharmCAT is also now available as a Docker image on Docker Hub.
• Various quality of life improvements for the preprocessor (see below for details).

Features

• data: update to CPIC v1.10 (0547340)
• preprocessor: set missing positions to ref (d80e8a7)

Bug Fixes

• 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)
• pharmcat: remove UGT1A1 special handling and add more SLCO1B1 examples (74c9ae8)
• preprocessor: update vcf header and properly sort vcf after normalization (e512bc3)
• preprocessor: validate bgzip (78ccd71)
• 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)

v1.1.0

1.1.0 (2021-10-14)

This release adds the PharmCAT preprocessor!

Features

• 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)

Bug Fixes

• 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)

v1.0.0

1.0.0 (2021-09-27)

⚠ BREAKING CHANGES

• The allele definition format has been updated and is not backwards compatible.
• updating to Java 14

Features

• 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)

Bug Fixes

• 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](69ea88e91edaae194871400d35d...

v0.8.0

0.8.0 (2021-03-31)

Features

• 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)

Bug Fixes

• 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)

Performance Improvements

• speed up VCF preprocessing (d5a847d)

Bugfix pre-release

This pre-release addresses a date formatting bug found in the v0.7.0 pre-release.

Release for publication doi:10.1002/cpt.1568

This release was created to correspond to the publication "Pharmacogenomics Clinical Annotation Tool (PharmCAT)" in Clinical Pharmacology & Therapeutics.

This release was used on a set of sample files from the GeT-RM project. You can find the data files and other supporting documents at the Stanford Digital Repository.

This release adds:

• new synthetic test VCFs for CYP2C19 & CYP3A5 to test the matcher
• fixes for some existing CYP2C19 test VCF files missing alt alleles
• many updates to the PharmCAT site
• a fix for reading definition files
• update to the CYP2C19 allele definitions that use rs72558189

Pre-release candidate

• updated CFTR allele handling
• updated TPMT allele handling
• add highlighting for called alleles that don't match alleles in the definition files
• fix bug for drug names in optional JSON report #18

Pre-release candidate

Improved UGT1A1 matching in certain phased samples.

Improved handling of conflicting calls for same position in the sample.