Changelog¶
1.2.2 (2024-12-18)¶
1.2.1 (2024-12-13)¶
Minor revisions
core¶
BAM
: added BAM file parserBED
andRegion
parsing updatedVFPVCF
: 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 gnomADCommonVariantsInSamplePairs
: 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 presetVCF
: fixed the methodapplySampleFilters()
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 SizeVCFHandling
: added MULTIALLELIC_DROPCannonical
: added deserialization from StringCannonical
: added isSNP()Genotpye
: added setTo(Genotype replacement)Genotpye
: added setToMissing()Region
: fixed Region had a compareTo, but did not explicitly implement the Comparable interfaceRegion
: added Annotation for the region (Extra column of a bed file)Region
: added setters for start, end and annotationRegion
: added boolean includes(Region r) to check if a region is fully included in another oneBed
: 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 functionSimulateVCFFromExisting
: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 managementPed
: 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)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 AFMergeVQSR
: added Functions that Merges SNP and INDEL results files from VQSRQC1078
: renamed toQC
FilterGnomADNFEFrequency
: added Function that filters on GnomAD NFE frequencies
filters¶
SampleFilter
: added Authorize VCF without samplesISKSVAF
: 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
: 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