Add a mode to test that the connection from Goby to R is working (requires JRI and R built
  with shared library support). The mode is called test-r-connection (tcr).
Remove dependency on R connection for somatic variation output. This change removes the p-value field.
Removed a little too much in the last commit.
Restore STRICT_SOMATIC filter.
Expose version number as a property and provide script to deploy or install Goby jar files to Maven
Add an option to the fasta-to-compact mode that will convert a set of files and concatenate the result to a single compact-reads file (see new --concat option).
Close streams after reading header and index
Close streams after reading header and index
Allow lenient import mode for TSV files. This makes it possible to convert TSV files to lucene.index when they have been created with Goby in the past with a \t character as last character of the column line.
Fix a bug that caused some slices to occur within annotations, despite the --annotation option being given on the command line. The problem was that the chromosome index was not obtained from the genome and was set to zero, always.
Improve javadoc.
Update CHANGES and version number for 2.3.4.1 release.