VEGA haplotype slices are non-reference now:

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.

unique genes method (for assembly patches), interactive does have an argument, other binaries default to 1 if nothing specified

merge in changes from ensembl-64 for retrieving non-reference slices. Don't need to supply a value for logappend, verbose, interactive and dry_run parameters

-nolog 1 will dump the output to stdout

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

Formatting of SYNOPSIS code.

Passes unit tests.