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CHANGELOG.rst

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Changelog

latest

v2.0.2 (2024-05-01)

  • Use en_US locale for running tests
  • Remove an extra t from the TSV header

v2.0.1 (2024-04-16)

  • Bug fix - When running with a VCF file, the TSV report will only include the diseases with a mutation in the associated gene, unless the --sdwndv is provided via CLI. Previously, the TSV reports included the diseases with no mutation regardless of the --sdwndv option.

v2.0.0 (2023-12-29)

  • Add prioritize command for running LIRICAL entirely from CLI
  • Support running analysis starting from both v1 and v2 phenopacket versions
  • Simplify the YAML input format
  • Enhance HTML report, add JSON output format
  • Split the codebase into several modules
  • Require Java 17 or better
  • Host documentation and API docs on github.io

v1.3.3 (2021-05-14)

  • Fixed output directory option for YAML input format

v1.3.2 (2021-04-09)

  • Fixed null pointer error in YAML output

v1.3.1

  • Update download URL for phenotype.hpoa
  • Update versions of multiple plugins/dependencies
  • Add option to simultaneously output HTML and TSV
  • maven wrapper

v1.3.0

  • Switch to picocli command line interface

v1.2.0

  • update to phenol 1.6.0 (note minor change to phenotype.hpoa format with '#' starting header line

v1.1.0

  • bugfix -- NCBI Gene ID ingest
  • update to phenol 1.5.0

v1.0.3

  • updated to phenol 1.4.2
  • added output of UCSC links to visualize variants
  • added some unit tests and fixed a few minor bugs

v1.0.1

  • updated to phenol 1.4.2
  • updated hpo annotation download URL

v1.0.0

  • Update to phenopacket-schema version 1.0.0
  • Improvements to HTML output

v1.0.0-RC2

  • fixed bug in YAML output
  • removing Ensembl option
  • Adding sparkline graphic to show posttest probability
  • various bug fixes

v1.0.0-RC1

  • Preparing first release
  • Adding posttest probability SVG to HTML output

v0.9.24

  • fixed bug in accessing the background data files within the JAR resource

v0.9.23

  • update to phenopacket-schema version 1.0.0-RC3
  • update to Exomiser 12.1.0
  • revisions to phenotype likelihood ratio algorithm for non-exact matching
  • more documentation

v0.9.22

  • update to phenol-1.4.1
  • Scoring for features excluded in query and disease.
  • Adding option to use Orphanet annotations

v0.9.21

  • ClinVar now requires assessment to be counted
  • bug-fix of "missing" genes
  • fixing SVG format for excluded phenotypes

v0.9.20

  • LIRICAL will terminate and emit an error warning if an unknwon HPO term is used in a phenopacket

v0.9.19

  • Fixed bug in counting pathogenic alleles (previously variants, not alleles, were being counted).
  • Adjusted calculations of phenotype likelihood ratios.

v0.9.18

  • Added evolutionary algorithm optimization
  • Bug fixes
  • YAML file analysis can do geno/pheno or pheno-only analysis

v0.9.16

  • Added code to simulate cases with template VCF and phenopackets
  • Fixed bug by which YAML file was not correctly setting prefix

v0.9.15

  • Changing name of ap to LIRICAL: LIkelihood Ratio Interpretation of Clinical AbnormaLities.
  • adding more unit tests

v0.9.14

  • update to phenopacket-schema version 0.4.0
  • update to Exomiser version 12.0.0
  • tweaking code for negative findings

v0.9.13

  • Streamlining some of the likelihood ratio code without changing logic
  • Adding routine for genotypes with more than 2 called pathogenic variants
  • tweaking HTML output
  • update to phenol 1.3.3
  • adding enforcer plugin

v0.9.11

  • Adding support for excluded phenotypes

v0.9.10

  • Compiling with Java 11
  • Simplifying and extending metadata and display in HTML

v0.9.8

  • Improved HTML/CSS formating
  • Simplifying command-line interface and adding Q/C checks for the existence of files with better error messages.

v0.9.7

  • Adding functionality for running LR2PG from a Phenopacket with VCF file path
  • now using phenol-1.3.2 from maven central
  • adding Q/C code for input files.

v0.9.4

  • Updating to phenol-1.3.2-SNAPSHOT
  • Allow ingest of OMIM/DECIPHER specifically to avoid redundant disease classes.
  • Improve HTML output template
  • Updated CLI to use JCommander

v0.9.3

  • Added phenopacket import class
  • fixed bug with genotype calculation for genes with multiple modes of inheritance

v0.9.2

  • Implemented Exomiser-style pathogenicity score for the analysis.

v0.9.1

  • Implemented likelihood ratio for variants with known ClinVar pathogenic status and corresponding tests with mockito

v0.9.0

  • First pre-release version
  • Adding genotypeExplanation for genotype LR score

v0.5.4

  • improved HTML template, adding some CSS and structure
  • improved display of information for differential diagnosis with no variants or no known disease gene

v0.5.2

  • adding functionality from previous G2GIT project
  • removing SpringBoot code
  • adding FreeMarker org.monarchinitiative.lirical.output for analysis of VCF+phenotype data

v0.4.4

  • refactored as SpringBoot application

v0.4.0

  • refactored to use phenol 1.1.0
  • adding code to simulate genotypes

v0.3.2

  • refactored TermId to remove superfluous interface and renamed ImmutableTermId to TermId
  • refactored TermSynonym to remove superfluous interface
  • adding support for alt term ids to Owl2OboTermFactory (class renamed from GenericOwlFactory)
  • adding support for database_cross_reference (usually PMID, ISBM, HPO, or MGI--added to term definitions)
  • refactoring to use phenol v.1.0.2

v0.2.2

  • Grid search over simulation parameters

v0.2.1

  • Finished version one of phenotype LR scheme

v0.0.3

  • fixed error with finding TermId in Disease2TermFrequency