Fix wrong coordinate from genomic indels, Fix no ref/alt errors. Add genePred support to allow users to easily load their own transcripts #53
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davmlaw
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Fix for #32 - Fix when no ref/alt
Fix for #50 - Fix genomic indels
Support .genePred files while keeping backwards compatability with refFlat (you never used the exon frames etc). With gff3ToGenePred (hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gff3ToGenePred) - this drastically increases the availability of transcripts - could be used to answer/close issues #26, #28, #39, #40
Optional disabling of "indels_start_with_same_base" error
Renamed get_coords -> get_ref_coords to be more explicit