Changed caching of unmapped reasons from new to store method to combat race conditions

[ENSCORESW-1057] Patch for get_overlapping_Genes for same-feature searches. Additional tests for this method added.

[ENSCORESW-1047] Altering column sizes for source in gene and transcript tables. Also patch test databases.

include alternative sequences with correct start/end

[ENSCORESW-1038] Fix bug in negative stranded assembly exceptions. Scoped variables were forgetting their new values and coming back undef.

ignoring phase creates more false positives than false negatives
also improves the overall exon mapping

added transcript_biotype in attrib field

Convenience accessors in GeneAdaptor. Main code in BaseFeatureAdaptor. fetch_all_nearest_by_Feature provides an exhaustive mechanism for finding nearby features and ordering them by proximity.

Massive overhaul of fetch_all_nearest_by_feature to handle all crazy edge cases. More tests, correct tests, more docs.

Introduce Nathan's unit tests and notes.