Merge pull request #1 from martinghunt/master

Add initial versions of gap filling and utr annotation scripts
Merge pull request #2 from martinghunt/master

Added support for snRNAs
Merge pull request #3 from martinghunt/master

Stop new UTRs being called that overlap existing genes in the reference
Add len method to gff object
Added transcript.total_exon_length method
added gene.longest_transcript_by_exon_length()
Added gene.remove_all_but_longest_transcript()
Deal with polypeptide records properly, by including them in transcripts
added script gff_keep_longest_transcripts
Merge pull request #4 from martinghunt/keep_longest_transcript_script

Keep longest transcript script
Added AUTHORS file
Merge pull request #5 from aslett1/master

Added AUTHORS file
Use smalt isntead of bowtie2
Add option --gap_abs_diff
Fix invalid SAM files