1. add predicate for haplotype slices;
2. workaround for issue with API where haplotype slices are non-reference
    but have no assembly exceptions;
3. fix map_assembly.pl so that it doesn't assume non-reference is a patch.

The other half of this commit is in ensembl-otter git.

Migration of fix for issue ENSCORESW-159. The wrong method was using in coding_region_start() resulting in incorrect UTR coordinates

ensembl-67'.

Sprout from master 2012-04-27 08:41:28 UTC Andrew Yates <ayates@ebi.ac.uk> 'Do not quote identifiers if they are going into a prepared statement. Otherwise we end up with odd results'
Delete:
    misc-scripts/protein_match/process_pmach.pl

Do not quote identifiers if they are going into a prepared statement. Otherwise we end up with odd results

Returns default mappers from a class level. Makes serialisation using Storable possible without bringing in B::Deparse

Added support for 'Active finishing' contigs. Removed hack for HG1211_PATCH unknown orientation (although GRC have bot provided a solution as yet) BUT added in a new hack for contig FP700111.21 which had to be retrieved from SVA (current version is FP700111.23).

Leaving lots of parameters empty. The pipeline can deal with this now and will use the correct defaults