Fix wrong coordinate from genomic indels, Fix no ref/alt errors. Add genePred support to allow users to easily load their own transcripts#54
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davmlaw wants to merge 49 commits intocounsyl:masterfrom
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This reverts commit 00a2205.
… exons are just a special case of alignments with no gaps
…0dup14 should pass but c.1727_1740dup9999 should fail
…o wrong coordinates and reference allele as it treats last digit as ref digit multiplying N that many times
…s. Be able to pass in pre-calculated values to save calculation if available
…when loading in utils
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See test_hgvs_names for what failed and is now fixed.
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