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## [0.8.0](v0.7.0...v0.8.0) (2021-03-31)

### Features

* add "label" field to Phenotyper output for diplotypes ([b92b914](b92b914))
* add new GenotypeInterpretation class ([c90e358](c90e358))
* add the reference flag to namedAllele objects ([f02d872](f02d872))
* add timer ([eb5c997](eb5c997))
* add warfarin and peginterferon back in to drug list ([18ed7f9](18ed7f9))
* change gene-phenotype to use new layout ([151de09](151de09))
* download to temp file ([5c46985](5c46985))
* enable Phenotyper to take either VCF input or NamedAlleleMatcher output JSON ([1631d52](1631d52)), closes [#39](#39)
* handle local files ([9d0c46b](9d0c46b))
* improve and expand outside call features ([e2eedfc](e2eedfc))
* include "comments" on recommendations in final report ([71ce411](71ce411))
* pull definitions from S3 and support ignored positions ([4702f04](4702f04))
* recursive output directory creation ([b547294](b547294))
* reporter update intermediate check-in ([33c560b](33c560b))
* update gene definition files ([141bed6](141bed6))
* update to latest CPIC drugs and phenotypes ([780a1f6](780a1f6))

### Bug Fixes

* adjust TPMT variant count ([dceb6ba](dceb6ba))
* appease javadoc ([6153145](6153145))
* avoid warning for transient Pattern in NamedAllele ([4e27107](4e27107))
* clear rsid map before rebuilding it ([d9973b8](d9973b8))
* combine duplicate position columns from CYP2D6 translation ([e70648d](e70648d))
* display number of files produced ([842414d](842414d))
* do not include data for anything involving blacklisted genes ([408f503](408f503))
* DPYD chromosomal HGVS name ([d82cb44](d82cb44))
* explicitly set date format ([876182e](876182e))
* fix bug when diplotypes are specified in reverse order (fixes DPYD bug) ([3849c47](3849c47))
* fix bug when overriding callable genes with outside calls ([85ad9f5](85ad9f5))
* fix bugs and performance in ExtractPositions ([95f3725](95f3725)), closes [#34](#34)
* fix CFTR tests to remove F508del and change "Reference" ([c50cfd4](c50cfd4))
* fix CYP2C9 *2/*3 unit test ([d82fd7e](d82fd7e))
* fix delete obsolete files ([11da562](11da562))
* fix DPYD integration test ([524c3c3](524c3c3))
* fix gene definition files to make reference allele be first ([0951f57](0951f57))
* fix NamedAlleleMather tests to account for changed allele names ([14f0f7f](14f0f7f))
* fix recommendation matching for multi-gene guidelines ([bd1ee0c](bd1ee0c))
* fix remove ignored positions not removing associated alleles ([9ca4a2c](9ca4a2c)), closes [#36](#36)
* fix unsafe operation compiler warning ([a081bb7](a081bb7))
* fix variant ordering bug ([ee7e1af](ee7e1af))
* fix VCF syntax for unspecified and deletion genotypes ([5b6ae8e](5b6ae8e))
* improve handling of "Unknown" calls ([a46866f](a46866f))
* names for position chr6:18132163 in TPMT ([39a99f7](39a99f7))
* remove "highlighted" drugs in final report ([4a1f9ef](4a1f9ef))
* remove "no calls" from sample files ([1fbb002](1fbb002))
* remove genes not used in recommendation match ([7c027d9](7c027d9))
* remove ignored positions from named alleles as well ([351979f](351979f))
* remove styling for Rx change in report ([4e89125](4e89125))
* remove tests for *60 UGT1A1 allele ([80fbd5f](80fbd5f))
* remove unnecessary variant allele options ([f931b89](f931b89))
* remove unused "g" option for PharmCAT CLI ([f161a67](f161a67))
* removed redundant convert_to_*.py scripts; condensed the scripts to one main script and one function library ([8ef9f21](8ef9f21))
* show genotype of "highlighted" variants in guideline section of report ([f2bf726](f2bf726)), closes [#31](#31)
* skip import of allele definitions that have all alleles ignored ([65dacd9](65dacd9))
* support ignored position exemptions ([5ecb6e1](5ecb6e1))
* switch to PEP8 code style, clean up output, add basic input error checking ([dac626c](dac626c))
* take chr## or ## (-> chr##) for CHROM ([9bce353](9bce353))
* update input argument ([2f57352](2f57352))
* update test cases to adjust for changes to allele definitions and exemptions ([cc0d997](cc0d997))

### Performance Improvements

* speed up VCF preprocessing ([d5a847d](d5a847d))
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PharmCAT

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A tool to extract all CPIC guideline gene variants from a genetic dataset (represented as a VCF file), interpret the variant alleles, and generate a report.

For more detail, read the PharmGKB blog post about PharmCAT or the article on GenomeWeb

Status

FOR TESTING ONLY

This application is under development and has not been officially released. Watch this repo or check the releases page for the official release

All technical requirements and documentation are available in the wiki.

PharmCAT is managed at Stanford University & University of Pennsylvania (NHGRI U24HG010862)

Contact

For technical questions or bug reports, file an issue.

For general questions about the PharmCAT project, contact pharmcat@pharmgkb.org.

Liability

⚠️ PhamCAT assumes no responsibility for any injury to person or damage to persons or property arising out of, or related to any use of PharmCAT, or for any errors or omissions. The user recognizes they are using PharmCAT at their own risk.