Changelog

1.2.4 (2025-02-07)

core

  • added : utils package and its classes used by InfoValueFilter

filters

  • implemented : InfoValueFilter that filters VCF line based on INFO values

1.2.3 (2025-01-31)

core

  • moved : some Functions changed package

functions

  • added : BedCoverageMerge that measures the number of samples with a depth of coverage above a threshold

1.2.2 (2025-01-21)

core

  • added : favicon in conf.py for ReadTheDocs

  • added : Genotype function getSumADOrElseDP to fall back on DP if AD metrics is missing

  • fixed : Some new Integer(string) replaced with Integer.parseInt(string)

1.2.1 (2024-12-13)

Minor revisions

core

  • BAM : added BAM file parser

  • BED and Region parsing updatedVFP

  • VCF : fixed getSamples() replaced with getSortedSamples(). The results were sorted by Hash instead of their order in the file

functions

  • Ignore “*” allele in most analyses

  • FilterF2 : Direct output instead of BufferedOutput (to avoid Out-of-Memory Exception)

  • FilterSeenInGnomAD : added Filters out variants that are seen in gnomAD

  • CommonVariantsInSamplePairs : added Count variants that are common to each sample pairs

filters

graphs

  • F2Graph : Highest value bar at 100% height

1.2.0 (2024-07-15)

core

  • BCF : added possibility to process BCF file (through a call to VCF)

  • Extensive Code rewrite to speed up BCF treatments

  • Canonical : fixed Left alignment (the event is always the leftmost possible)

  • Java 8 -> 11

functions

  • ExtractCanonical : added Function that convert a VCF to a list of canonical variant

1.1.0 (2024-05-16)

core

  • Extensive Code clean-up

  • removed GUI

  • Canonical : added overlap()

  • Info : added getFrequency(String key, int allele) where key is given by the calling function instead of being preset

  • VCF : fixed the method applySampleFilters() froze instead of dying if there was not enough columns in a line

functions

  • FilterFrequencies : changed removed limitation to pre-set populations

filters

  • ABHetMismatch : added Filters heterozygous genotypes that do not have 0.5-dev <= AB <= 0.5+dev

1.0.5 (2023-07-13)

core

  • Genotype : added getPl()

  • Function : added Print memory Heap Size

  • VCFHandling : added MULTIALLELIC_DROP

  • Cannonical : added deserialization from String

  • Cannonical : added isSNP()

  • Genotpye : added setTo(Genotype replacement)

  • Genotpye : added setToMissing()

  • Region : fixed Region had a compareTo, but did not explicitly implement the Comparable interface

  • Region : added Annotation for the region (Extra column of a bed file)

  • Region : added setters for start, end and annotation

  • Region : added boolean includes(Region r) to check if a region is fully included in another one

  • Bed : changed Regions in the Bed file are sorted through SortedList and not by hand anymore

functions

  • GetQCMetrics : added Function that gets all the Metrics used by the QC function

  • SimulateVCFFromExisting :added Function that Simulates a VCF File from an existing VCF File be mixing genotypes of samples from different ancestries

filters

1.0.4 (2022-08-04)

core

  • Main: optimized Plug-in management

  • Ped : added SEX_MALE, SEX_FEMALE, PHENO_UNAFFECTED, PHENO_AFFECTED values

  • VCF : fixed count of read/filtered variants in AtomicInteger (multi-threading and i++ don’t mix)

  • VEPAnnotation : fixed when a key is missing from the VEP annotation, the warning is only displayed once. If debug mode is activated, print stacktrace

functions

  • MaleFemale : added Functions that shows (among other information) male/female AF

  • MergeVQSR : added Functions that Merges SNP and INDEL results files from VQSR

  • QC1078 : renamed to QC

  • FilterGnomADNFEFrequency : added Function that filters on GnomAD NFE frequencies

filters

  • SampleFilter : added Authorize VCF without samples

  • ISKSVAF : added Filters Heterozygous Genotypes with V_AD/DP above of below a given threshold (should be in Plugin Project, but filters from Plugins are not yet supported)

1.0.3 (2020-12-09)

core

functions

  • QC1078 : fixed GitHub.Issues#2 non HQ variants were set to missing, so HQrate was equal to callrate. HQ parameter is removed (and now equal to callrate)

  • QC1078 : added AB check for genotypes. Failed ab check will set genotype to missing.

filters

other

  • getCustomRequirement : fixed typo in method name

1.0.2 (2020-11-05)

core

functions

  • AddAlleleBalance : fixed GitHub.Issues#1 [AB field not added for missing genotypes]

filters

other

1.0.1 (2020-09-30)

core

functions

  • CoverageStats : added

  • GzPaste : changed to use LineBuilder

filters

other

  • Gradle : added

1.0.0 (2020-09-24)

core

  • Fasta.getCharactersAt(String chromosome, long position, int length) : fixed to be thread safe

  • VEPConsequence : changed value index starts at 0 (for UNKNOWN) instead of -1

functions

  • CheckReference : added check for unexpected alleles ('\n' etc…)

  • CheckReference : added testing script

  • CommonGenotypes : moved to plugin Jar

  • CountInGnomAD : moved to plugin Jar

  • FrequencyCorrelation : changed VEPConsequence index starts at 0 instead of -1

  • GenerateHomoRefForPosition : added testing script

  • Kappa : added testing script

  • NumberOfCsqPerGene : changed VEPConsequence index starts at 0 instead of -1

  • PrivateVSPanel : added testing script

  • VCFToReference : added testing script

filters

other

  • CommonLib : fixed LineBuilder

  • Main.getVersion() : changed to read this CHANGELOG file

  • Main.main(String[] args) : moved to Run to enforce assert

  • FileParameter : fixed getExtension() returns String[]{} instead of null by default

  • Documentation : added versioning