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)