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