- Changing Guava version to 0.22
- Changing slf4j version to 1.7.24
- Changing log4j version to 2.8.2
- Adding experimental support for annotating with VCF files.
- Adding experimental support for annotating with tabix-indexed TSV files and dbNSFP.
- Integrating the advanced pedigree-based filters (useful for filtration to de novo variants).
- Making it possible to override database INI settings using user-specified INI files.
- Fixing stop loss annotation (#351).
- Finishing renaming of TranscriptInfo to TranscriptModel (#348).
- Upstream and downstream variant were considered "not off exome". They now are.
- Adding code for performing more advanced filtration/annotation filtering to de novo variants.
- Improving documentation of
MaxFreqAr
andMaxFreqAd
in header.
- Adding experimental support for annotating with VCF files
- Adding experimental support for annotating with tabix-indexed TSV files and dbNSFP
- Fixing bug that ignored variant filters for recessive annotation
- Fixin NPE problem with inheritance annotation
- Also counting number of variants on contigs
- Fixing counting bug that made UTR3 variants be counted as UTR5
- Fixing NPE in case of null variant annotations (e.g., unknown contig)
- Fixing a problem with normalization on variant annotation
- Fixing problem with default value of
CLNSIG
("25"
->"255"
)
- Incorporating gnomAD annotation into exclusion by frequency for inheritance filter (#343)
- Fixing header description for
MinAafHomAlt
andMaxAafHomRef
(#342)
- Checking that reference is given also for gnomAD VCF annotation
- Fixing language in mvn surfire plugin. Now mvn tests work on locale de_DE etc..
- Adding
--interval
argument for only processing a part of the file - Adding
statistics
command for computing statistics on variants in VCF file - Fixing bug in HGVS to VCF
- Better handling missing
.dict
file for HGVS to VCF translation - Adding
--annotate-as-singleton-pedigree
parameter for annotation of singleton pedigrees without pedigree file (single individual is assumed to be affected) - More friendly user message in case of unsorted files on inheritance mode annotation
- Interpretation of filters in compatible inheritance mode annotation
- Integrating new jannovar-filter into Jannovar CLI. Filtered genotypes will be passed into the inheritance filter as no-call.
- Adding annotation with ClinVar
- Printing warnings next to the annotations in
annotate-pos
- AR inheritance annotation of two siblings bugfix (no parents avaiable in comp.het mode) #314
- Adding functionality to add filters based on frequencies found in dbSNP and ExAC
- Adding back as module for threshold-based filtration. This module allows to create genotype-wise soft-filters for low coverage. Also, variants can be soft-filtered based on whether the genotype calls of all affected individuals are filtered out.
- Extending API to expose mendelian checks for comp het./ad alt (via
SubModuleOfInheritance
andMendelianInheritanceChecker
- Jannovar version is now written out to database file which allows better error checks and compatibility messages
- Un-deprecating
BestAnnotationListTextGenerator
andAllAnnotationListTextGenerator
classes, useful for text-based output formats - Changing behaviour of
VariantEffect.isOffExome()
and adding a variant that allows to decide between UTR on/off exome and non-consensus splice region on/off exome - Making the behaviour of overriding transcripts configurable at least in the code, using default to not do this any more
- Adding
WARNING_REF_DOES_NOT_MATCH_TRANSCRIPT
toAnnotationMessage
- Properly pushing through warnings from the annotators into the returned
VariantAnnotation
object - Pedigree files are now more compatible to the PLINK format
- whitespace separated instead of tab separated (read only, written as TSV)
- interpreting any value not in {1, 2} to be "unknown" sex instead (coded as 0) of throwing
- Fixing bug in transcript-to-genome translation, in HGVS the stop codon is not part of the CDS but in
TranscriptModel
it is - Optional interpretation of certain filters in GeneWiseMendelianAnnotationProcessor.
- Extending interface of
VariantContextAnnotator
for automatic error annotation generation, previously in jannovar-cli - Adding
VariantEffectHeaderExtender
class tojannovar-htsjdk
- Fixing bug with problems of unmodifiable Attributes (error annotation).
- Also writing out variant allele origin for dbSNP
- Adding annotation with COSMIC
- Fixing header description for exac database
- Fixing output of
DBSNP_CAF
to also contain reference allele AF - Adding annotation with ClinVar, can annotate all clinvar variants
- Removing this outdated module.
Use the classes in
de.charite.compbio.jannovar.mendel
instead
- all-new module for gathering statistics on VCF files
- Change email/organisations in master pom
GenotypeCalls.getGenotypeForSample()
returns a "no-call" genotype now instead ofnull
- fix to annotation with compatible mode of inheritance (#289)
- update to htsjdk 2.8.1
- removing requirement for proper contig
contig
lines in gene-wise gene annotation - fixing NPE in the case of no
contig
lines - improving error message on samples in VCF file that are not in pedigree
- fix to annotation with compatible mode of inheritance (#289)
- better overview on CLI help message
- if ref-fasta is not set properly a nicer error message will be shown.
- Fixing bug with problems of unmodifieable Attributes.
- Including Hom/Het/Hemi counds of ExAC (#295)
- update to htsjdk 2.8.1
This is a bugfix release.
- Manual loads version from central POM file now
- Adjusting manual links to point to
javadoc.io
- Fixing integration of HGNC into the downloaded databases
- For UCSC, HGNC records are searched based on the Entrez ID. If HGNC does not know the Entrez then only the Entrez ID from UCSC is written as additional ID.
- For RefSeq, linking is done through Entrez ID. If HGNC does not know the Entrez then only the Entrez ID from RefSeq is written as additional ID.
- For ENSEMBL linking is done through the ENSEMBL gene id. If this is not known to HGNC then no additional IDs are annotated.
- Fixing problem with
UnsupportedOperationException
injannovar-htsjdk
- replace charite email of p. robinson with the new one of jax
- Renaming
tx-to-chrom
tohgvs-to-vcf
, also in Java module names. - CLI changes such that one VCF input and one VCF output path can be used only
- Replacing apache commons-cli with argparse4j for a more modern and usable CLI
- Consistently writing out HUGO symbols for gene names, using the
hgnc_complete_set.txt
information downloaded when building the annotation DB - Upgrading from ENSEMBL-74 to ENSEMBL-75 for annotation database files
- Removing support for old Jannovar-style annotations (#241)
- Adding new command for annotating csv files (annotate-csv)
- Properly annotating Mendelian inheritance for intergenic variants
- downloading
hgnc_complete_set.txt
together with data sets,TranscriptModel
objects now consistently contain additional IDs - making ENSEMBL parsing more robust (falling back to transcript name if no transcript ID)
- fixing bug #248 for ENSEMBL that used
gene_id
forgene_name
- bugfix of NullPointerException in RefSeqParser while parsing refSeq curated
- bugfix space in SeqOID of SYNONYMOUS_VARIANT
- Update link to HGVS Nomenclature
- Now BestAnnotationListTextGenerator shows really the best and not all annotations!
- Documenting cli changes
- Adding additional sites contributing, FAQ and how to filter
- Better description of installations and quickstart
- this is gone, the functionality is now available as part of jannovar-cli
- this module is done, everything here is merged into jannovar-htsjdk
- The first version ships with support for dbSNP b147, ExAC 0.3, and the UK10K COHORT data base
- Initial version of this module, the aim is precise annotation from variant databases
- Updated
default_sources.ini
for latest patches of mouse and human genomes - Using one-letter amino acid code by default
- Removed slf4j2 warning at program startup
- Checking pedigree for compatibility with VCF file if given
- Adjusting API for annotating amino acid code by default
- Checking pedigree for compatibility with genotypes on Mendelian inheritance checking
- Refurbishing
Genotype
,GenotypeList
, andGenotypeListBuilder
inde.charite.compbio.jannovar.mendel
. - Moving
ModeOfInheritance
tode.charite.compbio.jannovar.mendel
. - Creating new package
de.charite.compbio.jannovar.mendel
with code for filtering for mendelian inheritance modes. - Renaming of
ModeOfInheritance.UNINITIALIZED
toModeOfInheritance.ANY
. - Fixing handling of invalid transcripts (e.g., incomplete 3' end)
- Adding
altGeneIDs
mapping toTranscriptModel
, makes data bases backwards incompatible. - Rewrite of GFF parsers for RefSeq and ENSEMBL.
- Bumping HTSJDK to 2.5.0, requiring Java 8 from now on.
- Removal of
AnnotationCollector
, priotization of variant effects is done after collecting all effect predictions now. - Fix for intronic variants between 5' or 3' UTRs. These variants were misclassified as
FIVE_PRIME_UTR_VARIANT
orTHREE_PRIME_UTR_VARIANT
. SequenceOntology implements new terms so that we can decide between the two UTR exon and intron variants. Now we haveFIVE_PRIME_UTR_EXON_VARIANT
orFIVE_PRIME_UTR_EXON_INTRON_VARIANT
(the same forTHREE_PRIME_UTR_EXON_VARIANT
orTHREE_PRIME_UTR_EXON_INTRON_VARIANT
).
- Adding better progress display with estimate of pending time.
- Adding support for annotating values from dbSNP VCF file (currently, only b147 is supported).
- Adding simple progress reporting (from verbosity level 2).
- Using Java 8 stream interface for
VariantContext
processing. - Removing support for Jannovar output format, VCF offer all features and more.
- Updating htsjdk to 1.142
- using simple logger of slf4j
- fixing version output in command line help
- changing command line interface to use more named arguments
- removing deprecated usage of commons-cli command line parser
- renaming of some internal classes and functions, fixing Javadocs
- fixing bug in
TranscriptSequenceChangeHelper
for reverse transcript (did not reverse complement alternate allele) - fixing bug in parsing GFF3 with some transcripts (e.g. GNAT1)
- less intrusive escaping in
ANN
field - renaming of some internal classes and functions, fixing Javadocs
- Updating htsjdk to 1.142
- renaming
InvalidGenomeChange
toInvalidGenomeVariant
- renaming
VariantContextAnnotator.buildGenomeChange
to.buildGenomeVariant
- renaming of some internal classes and functions, fixing Javadocs
- extending API of ProteinChange hierarchy for HGVS generation
- renaming of some internal classes and functions, fixing Javadocs
- Updating htsjdk to 1.142
- changing command line interface to use more named arguments
- adding two new functions to InheritanceCompatibilityChecker
- resolve boolean if passes inheritance into set where passed inheritances are stored
- Updating htsjdk to 1.142
- updating manual for 0.16 and using parameters for commands!
- updating readme for parameters
- making
CompatibilityCheckerAutosomalRecessiveHomozygous
public - using jannovar-hgvs for representing the changes
- more precise HGVS annotation in some cases
- predictions are wrapped in parentheses
- Mark everything that is related to the compatibility checkers as depricated (see new jannovar-inheritance-checker)
- adding module for parsing and representing HGVS-compatible nucleic and protein changes
- Updating htsjdk to 1.138
- Replacing depricatded method
VariantContext.getChr()
withVariantContext.getContig()
- Updating htsjdk to 1.138
- Replacing depricatded method
VariantContext.getChr()
withVariantContext.getContig()
- Updating commons-cli to 1.3.1
- Bugfix detecting autosomal chromosomes
- Bugfix with handling variant files with a leading "chr" in the contig.
- Adding this new module.
- Replaces the compatibility checker oh jannobvar-core.
- Now runs with VariantContext (htsjdk) instead of Jannovar Genotypes
- Use
InheritanceCompatibilityChecker.Builder
to buildInheritanceCompatibilityChecker
. - Use the method
getCompatibleWith
of theInheritanceCompatibilityChecker
with a List ofVariantContext
. - The method will return all
VariantContext
that matches the inheritance. If no variant matches the List is empty.
- Refactoring
VariantWiseInheritanceFilter
to handle the newInheritanceCompatibilityChecker
. - Rewrite
GeneWiseInheritanceFilter
to handle the newInheritanceCompatibilityChecker
. - Updating htsjdk to 1.138
- Replacing depricatded method
VariantContext.getChr()
withVariantContext.getContig()
- Adapting program to the
GeneWiseInheritanceFilter
andVariantWiseInheritanceFilter
(see jannovar-filter) - Updating commons-cli to 1.3.1
- Changing cli option inheritance-mode to multiple args (Now you can check multiple inheritances at once)
- Improving output file generation, jannovar-cli now uses the same extension as in the input and the infix is configurable instead of being fixed to ".jv".
- Default extension is ".vcf.gz" instead of ".vcf" now.
- Fixing label for
FRAMESHIFT_VARIANT
inVariantEffect
. - Moving CompatibilityCheckerException to package
...jannovar.pedigree.compatibilitychecker
- Fixing bug in transcript coordinate projection.
- Renaming
TranscriptSequenceChangeHelper.getCDSWithChange
to.getCDSWithGenomeVariant
. - Renaming
*.getChange()
to*.getGenomeVariant()
- Renaming
VariantAnnotator.buildAnnotationList
to.buildAnnotations
,VariantContextAnnotator.buildAnnotationList
to.buildAnnotations
, andVariantContextAnnotator.buildErrorAnnotationList
toVariantContextAnnotator.buildErrorAnnotations
- VariantAnnotations does not implement
List<Annotation>
any more - Adding
VariantAnnotations.getAnnotations
- Renaming
AnnotationList
toVariantAnnotations
- changing treatment of insertions at exon/intron junctions; they are considered as intronic insertions now that affect splicing
- converting
GenomeVariant
ofAnnotationList
to always be on the forward strand after construction ofAnnotationList
- deprecating the
{,All,Best}AnnotationTextGenerator
classes
- Moving
JannovarOptions
into jannovar-cli. - Displaying online help on unknown Jannovar command.
- Fixing
NullPointerException
bug for local paths. - Switching to official HTSJDK release and version 0.128.
- Writing out annotation about Jannovar call and version into the VCF file.
- Added option
--no-3-prime-shifting
to disable shifting towards the 3' end of the transcripts. - Added option
--no-escape-ann-field
to disable escaping of theANN
INFO
field. - Variants in
ANN
field are now annotated with proper Sequence Ontology terms.
- Modified
VariantContextWriterConstructionHelper
to allow explicit disabling of index creation. - Modified
VariantContextAnnotator
for adjustment to the new Exomiser. - Switching to official HTSJDK release and version 0.128.
- Changing
VariantContextWriterConstructionHelper
to allow writing out of additional header lines. - Added option to
VariantContextAnnotator#Options
for disabling 3' shifting. - Modified
VariantContextAnnotator
allowing to disable escaping of theANN
INFO
field.
- Moving
JannovarOptions
into jannovar-cli. - Renaming
ACompatibilityChecker
andICompatibilityChecker
. - Adding
GenomePosition.differenceTo(GenomeInterval)
. - Renaming package
de.charite.compbio.jannovar.io
tode.charite.compbio.jannovar.data
- Renaming
AnnotationLocation.toHGVSString
to.toHGVSChunk
. - Adding
Pedigree.subsetOfMembers
- Renaming
GenomeChange
toGenomeVariant
, same with types having the same prefix. - Introducing
DatasourceOptions
for configuring data download. - Removing support for using
"-"
as REF or ALT value. - Making previous
public final
membersprivate final
(orprotected final
) and adding getters for read-only access to them. - Removing position type member of
CDSInterval
. - Using type
Strand
instead of'+'
and'-'
, requires database rebuild. - Adding enum
Strand
withPLUS
andMINUS
values. - Adding
VariantEffect.isOffExome
and updatingVariantEffect.isOffTranscript
. - Removing
genomeRegion
member fromGenotypeList
. Also, adjusting the pedigree compatibility checkers for this, the check for being on the X chromosome has to be performed outside the checker now. VariantList.getHighestImpactEffect
now returnsVariantEffect#SEQUENCE_VARIANT
if no annotation can be found.VariantList
implements theList<Annotation>
interface now and theentries
member has become private.- Adding
VariantEffect#SEQUENCE_VARIANT
for variants with unknown effects. GenomeChange.toString()
now always converts to forward strand.- Fixing bug in
Annotation
and enforcing forward strandGenomeChange
instances. - Updates to the manual.
JannovarData
now also stores a mapping from transcript accession toTranscriptModel
and from gene symbol toTranscriptModel
.- Adding functionality for conversion from CDS to transcript and genome position and tests.
- Adding
AnnotationBuilderOption
object that allows disabling of 3' shifting towards the transcript. - Adding
JannovarOptions#escapeAnnField
. - Renaming
VariantType
toVariantEffect
- Changing
VariantType
to use proper Sequence Ontology terms. Legacy names can be obtained throughVariantType#getLegacyName
. - Spliting
CompatibilityCheckerXRecessive
intoCompatibilityCheckerXRecessiveCompoundHet
andCompatibilityCheckerXRecessiveHomozygous
. Now all inheritance checkers ar ready to use (AR,XR,AD,XD) - move all pedigree compatibility checkers from
de.charite.compbio.jannovar.pedigree
tode.charite.compbio.jannovar.pedigree.compatibilitychecker
and divide it into ar,xr,ad,xd. - generate interface
ICompatibilityChecker
for pedigree compatibility checkers. - Combine compatibility fields and methods in an abstract class
ACompatibilityChecker
to unify methods, builders, and fields.
- Splitting into
jped-cli
andjannovar-filter
- Changing public final members to accessors.
jannovar-filter
now has the Jannovar DB as the mandatory first argument.
- Changing public final members to accessors.
- Started bridge module between Jannovar and HTSJDK.
- Started tool for mode of inheritance--based filters.
- Splitting out bridge module between jannovar-core and HTSJDK to jannovar-htsjdk.
- Adding implementation of variant annotation standard 1.0.
- Adding unit tests for jannovar-cli.
- Fixing problem with empty
INFO
fields in output. - Adding back
--output-dir
to jannovar-cli. - Writing output parallel to input file by default.
- Adding
-v
and-vv
command line options. - Fixing problems with block substitution (delins) case (#87).
- Adding initial support for the transcript support level feature of the new VCF annotation standard (only in very recent ENSEMBL releases, apparently).
TranscriptModel#geneID
is now aString
- Update in various classes, e.g. Annotation.
- Fixing bug in PED parsing (empty lines are properly skipped now).
- More tests and fixes for the inheritance compatibility checkers.
- Updating
Annotation
for the variant annotation standard. TranscriptPosition
andTranscriptInterval
use zero-based positions now.- Reordering values of
VariantType
. - Somewhat renaming
VariantType
method names. - Removing the
VariantType#size
function in favor of astatic public
final
member. - Using log4j/slf4j for I/O in jannovar-core.
- Adding
PrintStream
as parameter toJannovarOptions#print
. - Compressing serialized file.
- Changing namespace to
de.charite.compbio.jannovar
. - Making
VariantType#priorityLevel
a non-static member. - Renaming
TranscriptInfo
toTranscriptModel
. - Moving
HG19RefDictbuilder
from tests to main. - Using
ImmutableMap
inTranslator
for small performance improvements. - Using
StringBuilder
-based concatenation of strings for generation of HGVS strings etc. since this is much faster than usingString#format
. GenomePosition
andGenomeInterval
use zero-based coordinates internally now.