v1.1.16

As always, see the JunctionSeq homepage for installation instructions.

Minor bugfixes: (thanks to Warren McGee)

• When making html summary files with "use.multigene.aggregates" genes set to TRUE,
  JunctionSeq will use shortened html file names in order to avoid filename length
  limitations on certain filesystems when there are numerous genes overlapping with
  one another. Aggregate gene names will be truncated to only include the first and
  last member genes iff there are more than 2 member genes, with a "..." in between.
• If minimalImageFilenames is FALSE, then Image files will similarly be renamed. Otherwise
  they will be reduced in size even further, as per the v1.1.10 update. You can
  control the naming of the png files using the options: "minimalImageFilenames",
  "name.files.with.geneID", and "number.plots"
• Fixed a bug in the phenotype table on the HTML index page.

Various minor "quality-of-life" improvements:

• When available, gene names will be included in all tables.
• The main index data table now includes mouseover text describing each column.
• Added additional information to each plot page.
• Added word wrapping to aggregate genes in the main index tables (thanks to Warren McGee).

In addition: Added further test cases to the testSuite:

• Added a legacy version of output from QoRTs v0.3.17, to test backwards-compatibility.
• Added test cases that test the new functionality.
• Added more genes to the "tiny" dataset in the JctSeqData package. This dataset is used in the examples and in the test suite. It now includes 3 "aggregate genes", which are composed of multiple genes that overlap. This allows fast testing of the "use.multigene.aggregates" parameter in the test suite.