# Changelog ## 1.0.4 (2020-12-16) ### core * ```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) ### 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``` ### filters ### other ## 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