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