CHANGELOG.md

Jannovar Changelog

v0.23

overall

• Changing Guava version to 0.22
• Changing slf4j version to 1.7.24
• Changing log4j version to 2.8.2

jannovar-cli

• 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.

jannovar-core

• Fixing stop loss annotation (#351).
• Finishing renaming of TranscriptInfo to TranscriptModel (#348).
• Upstream and downstream variant were considered "not off exome". They now are.

jannovar-filter

• Adding code for performing more advanced filtration/annotation filtering to de novo variants.
• Improving documentation of MaxFreqAr and MaxFreqAd in header.

jannovar-vardbs

• Adding experimental support for annotating with VCF files
• Adding experimental support for annotating with tabix-indexed TSV files and dbNSFP

jannovar-filter

• Fixing bug that ignored variant filters for recessive annotation

v0.22

jannovar-htsjdk

• Fixin NPE problem with inheritance annotation

jannovar-statistics

• 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)

jannovar-vardbs

• Fixing a problem with normalization on variant annotation
• Fixing problem with default value of CLNSIG ("25" -> "255")

jannovar-filter

• Incorporating gnomAD annotation into exclusion by frequency for inheritance filter (#343)
• Fixing header description for MinAafHomAlt and MaxAafHomRef (#342)

jannovar-cli

• Checking that reference is given also for gnomAD VCF annotation

v0.21

all

• Fixing language in mvn surfire plugin. Now mvn tests work on locale de_DE etc..

jannovar-cli

• 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

jannovar-filter

• 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.

jannovar-core

• Extending API to expose mendelian checks for comp het./ad alt (via SubModuleOfInheritance and MendelianInheritanceChecker
• Jannovar version is now written out to database file which allows better error checks and compatibility messages
• Un-deprecating BestAnnotationListTextGenerator and AllAnnotationListTextGenerator 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 to AnnotationMessage
• 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

jannovar-htsjdk

• 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 to jannovar-htsjdk
• Fixing bug with problems of unmodifiable Attributes (error annotation).

jannovar-vardbs

• 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

jannovar-inheritance-checker

• Removing this outdated module. Use the classes in de.charite.compbio.jannovar.mendel instead

jannovar-stats

• all-new module for gathering statistics on VCF files

v0.20

all

• Change email/organisations in master pom

jannovar-core

• GenotypeCalls.getGenotypeForSample() returns a "no-call" genotype now instead of null

jannovar-htsjdk

• fix to annotation with compatible mode of inheritance (#289)
• update to htsjdk 2.8.1

jannovar-cli

• 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.

jannovar-vardbs

• Fixing bug with problems of unmodifieable Attributes.
• Including Hom/Het/Hemi counds of ExAC (#295)
• update to htsjdk 2.8.1

v0.19

This is a bugfix release.

manual

• Manual loads version from central POM file now
• Adjusting manual links to point to javadoc.io

jannovar-core

• 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 in jannovar-htsjdk

v0.18

all

• replace charite email of p. robinson with the new one of jax

jannovar-cli

• Renaming tx-to-chrom to hgvs-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)

jannovar-htsjdk

• Properly annotating Mendelian inheritance for intergenic variants

jannovar-core

• 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 for gene_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!

Manual

• Documenting cli changes
• Adding additional sites contributing, FAQ and how to filter
• Better description of installations and quickstart

v0.17

jped-cli

• this is gone, the functionality is now available as part of jannovar-cli

jannovar-filter

• this module is done, everything here is merged into jannovar-htsjdk

jannovar-vardbs

• 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

jannovar-cli

• 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

jannovar-core

• Adjusting API for annotating amino acid code by default
• Checking pedigree for compatibility with genotypes on Mendelian inheritance checking
• Refurbishing Genotype, GenotypeList, and GenotypeListBuilder in de.charite.compbio.jannovar.mendel.
• Moving ModeOfInheritance to de.charite.compbio.jannovar.mendel.
• Creating new package de.charite.compbio.jannovar.mendel with code for filtering for mendelian inheritance modes.
• Renaming of ModeOfInheritance.UNINITIALIZED to ModeOfInheritance.ANY.
• Fixing handling of invalid transcripts (e.g., incomplete 3' end)
• Adding altGeneIDs mapping to TranscriptModel, 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 or THREE_PRIME_UTR_VARIANT. SequenceOntology implements new terms so that we can decide between the two UTR exon and intron variants. Now we have FIVE_PRIME_UTR_EXON_VARIANT or FIVE_PRIME_UTR_EXON_INTRON_VARIANT (the same for THREE_PRIME_UTR_EXON_VARIANT or THREE_PRIME_UTR_EXON_INTRON_VARIANT).

jannovar-cli

• 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.

v0.16

jannovar-cli

• 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

jannovar-core

• 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

jannovar-htsjdk

• Updating htsjdk to 1.142
• renaming InvalidGenomeChange to InvalidGenomeVariant
• renaming VariantContextAnnotator.buildGenomeChange to .buildGenomeVariant
• renaming of some internal classes and functions, fixing Javadocs

jannovar-hgvs

• extending API of ProteinChange hierarchy for HGVS generation
• renaming of some internal classes and functions, fixing Javadocs

jped-cli

• Updating htsjdk to 1.142
• changing command line interface to use more named arguments

jannovar-inheritance-checker

• adding two new functions to InheritanceCompatibilityChecker
• resolve boolean if passes inheritance into set where passed inheritances are stored
• Updating htsjdk to 1.142

manual

• updating manual for 0.16 and using parameters for commands!
• updating readme for parameters

v0.15

jannovar-core

• 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)

jannover-hgvs

• adding module for parsing and representing HGVS-compatible nucleic and protein changes

jannover-htsjdk

• Updating htsjdk to 1.138
• Replacing depricatded method VariantContext.getChr() with VariantContext.getContig()

jannovar-cli

• Updating htsjdk to 1.138
• Replacing depricatded method VariantContext.getChr() with VariantContext.getContig()
• Updating commons-cli to 1.3.1

jannover-inheritance-checker

• 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 build InheritanceCompatibilityChecker.
• Use the method getCompatibleWith of the InheritanceCompatibilityChecker with a List of VariantContext.
• The method will return all VariantContext that matches the inheritance. If no variant matches the List is empty.

jannover-filter

• Refactoring VariantWiseInheritanceFilter to handle the new InheritanceCompatibilityChecker.
• Rewrite GeneWiseInheritanceFilter to handle the new InheritanceCompatibilityChecker.
• Updating htsjdk to 1.138
• Replacing depricatded method VariantContext.getChr() with VariantContext.getContig()

jped-cli

• Adapting program to the GeneWiseInheritanceFilter and VariantWiseInheritanceFilter (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)

v0.14

jannovar-cli

• 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.

jannovar-core

• Fixing label for FRAMESHIFT_VARIANT in VariantEffect.
• 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, and VariantContextAnnotator.buildErrorAnnotationList to VariantContextAnnotator.buildErrorAnnotations
• VariantAnnotations does not implement List<Annotation> any more
• Adding VariantAnnotations.getAnnotations
• Renaming AnnotationList to VariantAnnotations
• changing treatment of insertions at exon/intron junctions; they are considered as intronic insertions now that affect splicing
• converting GenomeVariant of AnnotationList to always be on the forward strand after construction of AnnotationList
• deprecating the {,All,Best}AnnotationTextGenerator classes

v.0.13

jannovar-cli

• 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 the ANN INFO field.
• Variants in ANN field are now annotated with proper Sequence Ontology terms.

jannovar-htsjdk

• 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 the ANN INFO field.

jannovar-core

• Moving JannovarOptions into jannovar-cli.
• Renaming ACompatibilityChecker and ICompatibilityChecker.
• Adding GenomePosition.differenceTo(GenomeInterval).
• Renaming package de.charite.compbio.jannovar.io to de.charite.compbio.jannovar.data
• Renaming AnnotationLocation.toHGVSString to .toHGVSChunk.
• Adding Pedigree.subsetOfMembers
• Renaming GenomeChange to GenomeVariant, 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 members private final (or protected 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 with PLUS and MINUS values.
• Adding VariantEffect.isOffExome and updating VariantEffect.isOffTranscript.
• Removing genomeRegion member from GenotypeList. 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 returns VariantEffect#SEQUENCE_VARIANT if no annotation can be found.
• VariantList implements the List<Annotation> interface now and the entries 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 strand GenomeChange instances.
• Updates to the manual.
• JannovarData now also stores a mapping from transcript accession to TranscriptModel and from gene symbol to TranscriptModel.
• 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 to VariantEffect
• Changing VariantType to use proper Sequence Ontology terms. Legacy names can be obtained through VariantType#getLegacyName.
• Spliting CompatibilityCheckerXRecessive into CompatibilityCheckerXRecessiveCompoundHet and CompatibilityCheckerXRecessiveHomozygous. Now all inheritance checkers ar ready to use (AR,XR,AD,XD)
• move all pedigree compatibility checkers from de.charite.compbio.jannovar.pedigree to de.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 classACompatibilityChecker to unify methods, builders, and fields.

jannovar-filter

• Splitting into jped-cli and jannovar-filter
• Changing public final members to accessors.
• jannovar-filter now has the Jannovar DB as the mandatory first argument.

jannovar-htsjdk

• Changing public final members to accessors.

v0.12

jannovar-htsjdk

• Started bridge module between Jannovar and HTSJDK.

jannovar-filter

• Started tool for mode of inheritance--based filters.

jannovar-cli

• 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).

jannovar-core

• 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 a String
• 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 and TranscriptInterval use zero-based positions now.
• Reordering values of VariantType.
• Somewhat renaming VariantType method names.
• Removing the VariantType#size function in favor of a static public final member.
• Using log4j/slf4j for I/O in jannovar-core.
• Adding PrintStream as parameter to JannovarOptions#print.
• Compressing serialized file.
• Changing namespace to de.charite.compbio.jannovar.
• Making VariantType#priorityLevel a non-static member.
• Renaming TranscriptInfo to TranscriptModel.
• Moving HG19RefDictbuilder from tests to main.
• Using ImmutableMap in Translator for small performance improvements.
• Using StringBuilder-based concatenation of strings for generation of HGVS strings etc. since this is much faster than using String#format.
• GenomePosition and GenomeInterval use zero-based coordinates internally now.

v0.11