- general: display error messages if incorrect input parameters are used
- general: added input parameter (-m or --method) to select method (genomic vs. histogram)
- general: minor bugfixes
- general: improved documentation (both: source code and command line help)
- histogram mode: added input parameter (-w or --window) to select window size
- histogram mode: added input parameter (-b or --bins) to select the number of bins
- histogram mode: check whether there are overlapping features in the gff/gtf files. The histogram method only works with non-overlapping features; otherwise the script throws an error message and stops the execution.
- tests: initially started using the hg19.chr19.fasta and hg19.chr19.gtf test data in the repository but the gtf file contains overlapping features! I have created really small fasta and gtf files to test this script but I am not going to upload them yet to the CGAT repository.