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@julesjacobsen julesjacobsen released this 13 Feb 17:05
· 2758 commits to master since this release
6.0.0
23d6ea8

Core API changes:

  • Package tidy-up - all packages are now use their maven package name as the root package for that project.
  • PhenixPriority now dies immediately and with an informative message if no HPO terms are supplied.
  • Added NONE PriorityType for when you really don't want to run any prioritiser.
  • Re-named the ExomiserMouse and ExomiserAllSpecies prioritisers to their published Phive and HiPhive names.
  • Removed unused List requirement from writers.
  • TSV output now comes in TSV_GENE and TSV_VARIANT flavours.
  • Removed unused getBefore and getAfter methods from Priority interface.
  • Removed getConnection and setConnection from Priority interface as these were only used by some prioritisers.
  • Prioritisers requiring database access now use a DataSource rather than a direct connection.
  • Added getRowIndexForGene(entrezGeneId) and getColumnMatrixForGene(entrezGeneId) methods to DataMatrix.
  • Removed getRowToEntrezIdIndex from DataMatrix.
  • Refactored ExomeWalkerPriority and ExomiserAllSpeciesPriority to use new DataMatrix methods.

CLI changes:

  • Added 'none' type prioritiser for when you really don't want to run any prioritiser.
  • Exomiser will now show the help options when no parameters are supplied.
  • New test settings files for different prioritisers and the batch file.
  • Changed input parameters these are optional switches:
    --remove-path-filter-cutoff to --keep-non-pathogenic
    --remove-off-target-syn to --keep-off-target
  • Renamed somewhat misleading example.settings to template.settings to reflect it's intended use.
  • TSV output now comes in TSV_GENE and TSV_VARIANT flavours.
  • Added missing ehcache.xml to the distribution.
  • Switched PostgreSQL driver to use pgjdbc-ng which allegedly has better performance.
  • Consolidated JDBC Connection pool to use HikariCP.
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