Add fuzzy matching on synonyms

fetch_by_region allows fuzzy matching on the end of the given seq_region_name. Required for compara's HAL parsing.

Typo in Identity Xref function, variable should be $xref_end, not $xref_start

Master

If $load_transcripts is true, do not do lazy loading in any case (including when the number of genes is 1).

Fixed example to create and edit an AltAlleleGroup.

Updated fetch_all_by_Transcript method to optionally filter by featur…

If $load_exons is true, do not do lazy loading in any case (including when the number of transcripts is 1).

If $load_exons is true, do not do lazy loading in any case (including when the number of transcripts is 1).

Check that translations exist before comparing the sequences

If a translation object does not exist, we do not try to access its sequence

Check that an analysis exists before calling logic_name on it, needed for testing where a full object might not exist. And just good sanity.

New Transcript added to the test file transcript.txt. So updated the tests that checks for the transcript count.

Updated fetch_all_by_Transcript method to optionally filter by feature_type (dna_align or protein_align features)

Add seq_region_start and seq_region_end to Slice, as a Slice is always relative (or is) a toplevel coordinate system, a simple alias to start/end() are possible.

New attrib table for dna_align_features