v0.18

As with all recent releases, Jannovar is best installed through Maven Central.
Alternatively you can directly download the compiled jannovar-cli-0.18.jar.

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

As with all recent releases, Jannovar is best installed through Maven Central.
Alternatively you can directly download the compiled jannovar-cli-0.17.jar.

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

As with all recent releases, Jannovar is best installed through Maven Central.
Alternatively you can directly download the compiled jannovar-cli-0.16.jar.

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

As with all recent releases, Jannovar is best installed through Maven Central.

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

• 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

Some smaller fixes to 0.13.

v0.13

Major refactorization and new functionality. See the CHANGELOG.md for details.

v0.12

This release provides two JAR files with executable code:

• jannovar-cli is a command line interface to the Jannovar functional annotation program
• jannovar-filter is a command line interface to filtration of VCF files by compatibility with a selected mode of inheritance

If you want to use Jannovar as a library, the POM file also gives you the jannovar-core module for the functional annotation and the jannovar-htsjdk module which allows for directly annotating VariantContext objects from HTSJDK.

v0.11

First release after Jannovar rewrite. Meant for public testing.