Bed file reading hotfix

Fixed interval incongruencies between BED file and samtools Interval. (0 based vs 1 based)

Additional small check for a possible empty 'name' column (column[3]) where there may be further info in the bed file that could break the parsing (score - column[4] etc).

Confidence fix, Hotfixes and logging

• Fixed confidence calc formula in line with paper
• Trans subscores are only doubled if more than 1 evidence found
• Fixed VCF writing bugs including last line not being printed
• Logging improvements and better error messages

Confidence Overhaul

Overhaul of the confidence system to fully mirror the idea presented in the paper.

Release 1.0.0

Initial release