Changelog¶

1.1.0 (2024-05-16)¶

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

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

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

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

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

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

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)

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.

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

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

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

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