CHANGELOG

15-068
020315 - Added checks to parse annotation files and ensure that their format is
suitable for the pipeline.

020315 - Corrected errors that parsed chromosome
length header incorrectly adding NAs to GRange object chromosome length fields.

040315 - Added test script
         Added check to ensure NCBI repeat files aren't gzipped.

090315 - Edited file checks to allow different miRBase genome version formats and
trailing '*' in RepeatMasker files
         Edited manual pages
15-069
100315 - Edit scripts to conform with GenomicRanges > 1.10 (use of mcols etc.).
100315 - Add R-version check to ensure R 2.15.1 or later is used.

15-078
100315 - Improve error messages
190315 - Pipeline conforms to new Ensembl GTF layout (v77+) and can identify
         transcript_biotype successfully in both older and current systems
         Documentation improved to ensure -b is specified when running tRNAscan
         and tests implemented.
         Add example command to documentation.
         Change order of assembly to format miRBase files.

15-079
190315 - Corrected heirarchy typo
         File checks accept a trailing space in RepeatMasker files

16-264
280916 - Save version prior to GitHub upload

300118 - Correct mistake in the annotation-check script that used 
         a global variable when reporting errors in the GFF format.
         Although minor it made tracking problems in GFF files confusing.
         (v18-108)