This version slays fish and chicken.
"report-masked.py": find masked regions in a multifasta and report them as BED. "fix-splign-orf" now faster (dropped biopython).
Merge branch 'development'
BED format hotfix.

As per the UCSC specification:
The chromEnd base is not included in the display of the feature.
For example, the first 100 bases of a chromosome are defined as
chromStart=0, chromEnd=100, and span the bases numbered 0-99.
Improved parsing of multifastas.
Merge branch 'development'
Improved splign2bed.
Hard and soft masking.
Implemented recognition of soft and hard masking in report-masked.py
Bugfixes and improved logic.
Skip transcripts with no mapped exons.
Skip transcripts with no mapped exons.
File parsers are now from the Swiffe library.