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Jannovar Changelog

v0.42

jannovar-cli

  • Add a /annotate-var endpoint to the rest server that accepts POST method for annotating single variants.
    • Launch with jannovar-cli rest-server -d data/hg19_refseq.ser -d data/hg19_ensembl.ser
    • Then, query with request body { "source": "refseq", "assembly" : "hg19", "chr": "chr1", "pos": "111926150", "ref" : "GGCACTCCAGGGGACTA", "alt" : "G" } or { "source": "ensembl", "assembly" : "hg19", "chr": "chr1", "pos": "111926150", "ref" : "GGCACTCCAGGGGACTA", "alt" : "G" }
    • ?no-3-prime-shifting can also be sent as a query param to temporarily disable the shifting.

v0.41

jannovar-core

  • Fixing problem with annotating Dragen CNV VCF (#558)

v0.40

jannovar-core

  • Coding insertions are now annotated for splicing (#554)

jannovar-cli

  • Argument --no-3-prime-shifting had inverse meaning (#552). This has been fixed now.
  • Hook --no-3-prime-shifting argument with the rest server. If shifting is enabled, ?no-3-prime-shifting can be sent as a query param in the API request to temporarily disable the shifting.

v0.39

overall

  • Moved away from split between master and develop branch to using main branch
  • Fixing broken download links in README (#533)

jannovar-core

  • Adding support for mitochondrial genetic code (#501)
  • Fix problem with building ENSEMBL (#540)
  • Fix problem with HGVS-to-VCF (#539)

v0.38

overall

  • More bumping of log4j against log4shell exploit.

v0.37

overall

  • Adding support for parsing HGVS repeats.
  • Adding support for "chr2acc" chromosome to accession mapping.
  • Bumping log4j version against log4shell exploit.

v0.36

Highlight: Pre-Built Databases

We now provide pre-built databases via Zenodo. This addresses various issues that were caused by changing upstream data URLs. See README.md for details.

overall

  • Switching to Github Workflows for continuous integration.
  • Bumping a couple of dependencies.
  • Switching to JUNIT 5.
  • Pre-built databases are now available via Zenodo (see README.md for instructions). We provide shell scripts instead of using Java programs for downloading the files.

jannovar-core

  • Apply fix for (#498, PR #499 by @roland-ewald of @limbus-medtec). This fixes a problem with right-shifting deletions on amino acid sequences. See the tickes and merge request for details.
  • Fixing problem with GRCh38 RefSeq annotation / projection (#524).

jannovar-cli

  • Adding command vardb-import for importing annotations from VCF files into H2 database files.
  • Adding command vardb-list for listing annotation meta data from vardb-import.
  • Adding command vardb-annotate for annotating VCF files from Jannovar H2 database files.

jannovar-vardbs

  • Deprecating previous content of the package. The deprecated classes are due to be removed in v0.36.
  • Adding modules for importing VCF files into H2 database files, listing the meta data conents, and annotating VCF files.

jannovar-hgvs

  • Fixing parsing of unchanged (=) for nucleic acide sequences (#493).
  • Fixing issue with HGVS delins with del bases but no ins bases (#491).

v0.35

jannovar-core

  • Update Genotype internals to pre-calculate values.

jannovar-cli

  • Fixing default_sources.ini file.

v0.34

jannovar-cli

  • disabeling ensemble for mouse (does not work with an hgnc file)
  • updating broken links in download source file
  • Adding faMT genomes for all refseq annotations
  • bumping dependency on lombok

jannovar-core

  • Remove hard-coded chrMT renaming. Filenames for download that have a ? in their URL will be splitted and only the first part before the ? is used a file name in the download path.
  • Making faMT annotation for refSeq optional
  • Update RefSeq parser that does not run into null-pointer exceptions on mouse and rat genome (e.g. when no exon defines the gene name)
  • Fixing issue with block substitutions (#475).
  • Fixing RefSeq build to properly assign transcript model (use best match with alignment) in the case of duplicates.
  • Fixing issue in projection in the case of leading gaps (has no effect on CDS position prediction).
  • Adding TranscriptModel.getTrimmedSequence() that removes leading and trailing (unaligned in RefSeq) sequence.

jannovar-htsjdk

  • Bumping HTSJDK dependency to v2.20.3 because 2.20.0 has a bug in the VariantContextBuilder

v0.33

overall

  • Fixing ANN annotation field to have ./unbound cardinality.
  • Bumping several dependencies, including HTSJDK.

manual

  • Adding conda support in installation documentation
  • Fixing broken link in quickstart

jannovar-core

  • Fixing annotation of SVs that look like sequence variants (#456). Interpretation is to use the sequence variant annotation code now. This fixes a bug with annotating latest ClinVar for GRCh38.
  • Prevent Annotation.{getPutativeImpact,getPutativeImpact}() from returning null (#458).
  • Correctly parsing RefSeq mitochondrial transcripts. Bumping the required versin to 0.33-SNAPSHOT to higlight this (#463).

v0.32

overall

  • Changing log4j version to 2.11.2
  • Changing slf4j version to 1.7.25

jannovar-cli

  • Adding a simple REST server for annotating single variants.
    • Launch with jannovar-cli rest-server -d data/hg19_refseq.ser -d data/hg19_ensembl.ser
    • Then, query with /annotate-var/refseq/hg19/chr7/140453136/A/T or /annotate-var/ensembl/hg19/chr7/140453136/A/T

v0.31

jannovar-core

  • Introducing classes for representation of gapped sequences, alignments, and position projection.
  • Fixing bug in ENSEMBL transcript database generation (tx version was appended twice)
  • Adding flags for "has substitutions" and "has indels" to TranscriptModel that get filled for RefSeq transcripts.
  • Correctly parsing of RefSeq transcripts with indels.

jannovar-cli

  • Using HTTP protocol instead of FTP everywhere as it's possible (#451).
  • Fixing HGVS conversion for indels (#452).

v0.30

Bugfix release.

jannovar-core

  • Fixing interpretation of INFO/SVTYPE, urldecode and only use the first component after splitting at ":".
  • Interpreting SV type annotation for SV2 more correctly.

v0.29

jannovar-core

  • Putative impact of splice_region_variant has changed from MODERATE to LOW (see issue #439)
  • Decreasing log verbosity in one location when building database.
  • Fixing CDS region import in RefSeqParser
  • Putative impact of splice_region_variant has changed from MODERATE to LOW (see issue #439)
  • Fixing SV annotation using hg38/ucsc for transcripts without gene ID (see #444).
  • Adding support for rn6 RefSeq transcripts. Adding allowNonCodingNm directive for data source INI file to disable check that RefSeq NM transcript has CDS.
  • Adding versions to ENST accessions for ENSEMBL.

jannovar-vardbs

  • Bugfix: TSVAnnotator did not use end given column.

v0.28

jannovar-cli

  • Bumping ENSEMBL versions for GRCh37 and GRCh38.
  • Fixing sources information for updated ENSEMBL downloads.
  • For ENSEMBL, use ENSEMBL-provided mapping from ENSG to HGNC ID for Entrez ID assignment. This is necessary as Ensembl gene IDs turn out to be not so stable between hg37 and hg38 after all. Case in point: ENSG00000276141 vs. ENSG00000187667.
  • Adding --gene-ids argument to downloader for creating smaller databases (mostly for test purposes).
  • Adding SV support to jannovar-cli, includes tests.
  • Using ENSEMBL-provided mapping from ENSG to Entrez ID in the case HGNC mapping does not work.

jannovar-htsjdk

  • Adding SV support to jannovar-htsjdk
  • Bumping HTSJDK dependency to v2.18.2

jannovar-core

  • Changing upstream/downstream size to 5kbp.
  • Support for prioritizing RefSeq transcript on the PAR of chrX over those of chrY
  • Refactorizations to improve performace using EnumSet.
  • Extended VariantEffect for the effects of structural variants. Removing documentation that the effect is not used in Jannovar for some now interpreted ones. Also variant effect for non-coding variants is added using the current VEP predictions as a template.
  • Prohibiting creating GenomeVariant with symbolic alleles. Throwing new checked exception InvalidGenomeVariant case of error.
  • Fixing SO term ID for VariantEffect.DISRUPTIVE_INFRAME_DELETION
  • Correctly parsing transcript version for ENSEMBL when available (not available for b75/GRCh37).
  • Making transcript model building (for download) more memory efficient.

v0.27

jannovar-cli

  • Integrating support for thousand genomes VCF
  • Integrating thousand genomes/ExAc count limits into inheritance filter

jannovar-vardbs

  • Adding support for thousand genomes VCF

jannovar-htsjdk

  • Adding support for limiting genomes/ExAc counts into inheritance filter

v0.26

jannovar-cli

  • Making OneParentGtFiltered filter optional. The default setting to false (specify --one-parent-gt-filtered-filters-affected to enable).

jannovar-core

  • Moving variants in non-coding transcripts after UTR variants.

jannovar-hgvs

  • Fixing parser issue for nucleotide indels (#408).

jannovar-htsjdk

  • Obey the options.escapeAnnField parameter for escaping the variant effect in the ANN field.

v0.25

overall

  • Changing HTSJDK version to 2.14.3
  • Using the one letter amino acid code in HGVS representation as default (changes in core, hgvs, htsjdk and cli). Now the cli option --3-letter-amino-acids works as expected.

jannovar-cli

jannovar-vardbs

  • Replacing whitespace with string when annotating from TSV file.

jannovar-htsjdk

  • Fixing bug in GenomeRegionSequenceExtraction. Error reports always sequences from the first contig in the referebnce file and not the requested contig. Affects only the cli command hgvs-to-vcf.

v0.24

jannovar-cli

  • Fixing annotation with Polyphen prediction (data type)

overall

  • Changing HTSJDK version to 2.14.0
  • Codestyle improvements

jannovar-core

  • Fixing mendelian "bug" #393 (has no affect because check was not necessary)
  • New inheritance mode: mitochondrial
  • Bugfix ProgressBar (doPrint was always true)

jannovar-vardbs

  • Fixed problem with interpretation of Clinvar annotation origin.
  • Clinvar BEST_AC and BEST_AF are now named AC_POPMAX and AF_POPMAX to be consitent with gnomAD

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.
  • Adding mitochondrial filtering function (#362).

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