Changelog¶
1.0.4 (2020-12-16)¶
core¶
Ped
: added SEX_MALE, SEX_FEMALE, PHENO_UNAFFECTED, PHENO_AFFECTED valuesVCF
: 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 AFMergeVQSR
: added Functions that Merges SNP and INDEL results files from VQSRQC1078
: renamed toQC
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
: addedGzPaste
: changed to useLineBuilder
filters¶
other¶
Gradle
: added
1.0.0 (2020-09-24)¶
core¶
Fasta.getCharactersAt(String chromosome, long position, int length)
: fixed to be thread safeVEPConsequence
: changed value index starts at 0 (for UNKNOWN) instead of -1
functions¶
CheckReference
: added check for unexpected alleles ('\n'
etc…)CheckReference
: added testing scriptCommonGenotypes
: moved to plugin JarCountInGnomAD
: moved to plugin JarFrequencyCorrelation
: changedVEPConsequence
index starts at 0 instead of -1GenerateHomoRefForPosition
: added testing scriptKappa
: added testing scriptNumberOfCsqPerGene
: changedVEPConsequence
index starts at 0 instead of -1PrivateVSPanel
: added testing scriptVCFToReference
: added testing script
filters¶
other¶
CommonLib
: fixedLineBuilder
Main.getVersion()
: changed to read this CHANGELOG fileMain.main(String[] args)
: moved to Run to enforceassert
FileParameter
: fixedgetExtension()
returnsString[]{}
instead ofnull
by defaultDocumentation
: added versioning