Moved fix-orf (formerly fix-splign-orf.py) and spligntobed (formerly splign2bed.py) into wrapper script dobby-tools (methods are in their respective modules now).
report-masked now in wrapper script.
Removed old fix-splign-orf.py script.
Moved wmtobed (wm2bed) into wrapper script.
Conversion between formats.
HOW COULD I FORGET THE MAIN SCRIPT
Conversion between UCSC, NCBI, GenBank chromosome naming conventions.
Format parser calls changed according to swiffe restructuring.
Using updated swiffe.
Faking fastq files out of fasta.
GOING HARDMODE.
Merge branch 'development'
HARDMODE INTENSIFIES.