GitLab

[ENSCORESW-264] Can now handle odd sequence region names involving . - _ now. The supercontig names seemed to be a good source of these

Assignment bug; we did not want the cache assigned to the ID of the seq region but wanted the seq region id into a local variable. Fixed.

Made the circular slice code compartmentalised to just SliceAdaptor (making cache initalisation code easier) and we now only build circular slices when the seqregion it is based off is flagged as circular

toplevel location code can now deal with excessively large regions and shrinks them down to size if possible or rejects them.

not needed and move declaration of a statment handle to aviod having to
declare another one.

Slice::dbID().

<ensembl-dev@ebi.ac.uk> to <dev@ensembl.org>.

Added new option to method fetch_all which is include_lrg. By defualt lrg slices willl NOT be returned if this is not set (default is off) also since at present all lrg regions are non reference this flag must be set too to get the lrg regions.

added new method fetch_by_region_unique which returns the non duplicate regions. This is mainly for getting non duplicated regions like assembly patches or haplotype regions

Always de-reference the value got from get_mapping_path().
Found by Magali.

Formatting of SYNOPSIS code.

Passes unit tests.