pick was sorting on biotype the wrong way round
fix inheritance
Improve logic of computing variant site based on cigar string

Add changes to how the postion of a variant based on a cigar string
is computed. Changes help to summarise deletion and insertion operations.
Fix indentation
Consider clipped nucleotides in computation of alignment score
Fix indentation
Fix indentation
Fix indentation
Fix indentation
Fix indentation
+doc, 'sample' to 'population', +link and sorted

I'm only changing the documentation here, not SQL!

The inline documentation is used to generate http://www.ensembl.org/info/docs/api/variation/variation_schema.html#allele

The documentation for a couple of columns has outdated references to 'samples' where the table now uses population_id.

I added a link to the submitter_handle table, so all FKs are now linked under the 'see also' list.

I re-ordered the columns to match what's in the SQL.

I re-ordered the 'see also' list to match the order of the columns.
* change added so users can limit the TranscriptEffect analysis to certain
  biotypes. If no biotype has been supplied, all genes are fetched
  ( default behaviour).
* removed use of Data::Dumper
fix typo
fix chromosome sorting
This script dumps out all genotypes

It uses a join from variation_feature to compressed_genotype_var
and dumps out the genotypes (as genotype_ids) joined to the
variation_feature location columns; the idea is this data can be
used to reconstitute compressed_genotype_region.
script to compress genotypes dumped by ../export/dump_compressed_genotypes.pl
Clean up and add brief description of script

Conflicts:

	scripts/export/dump_compressed_genotypes.pl
allow flag_pick, like pick but just indicates with flag
add code to retrieve HGNC ID, which is more stable than the gene symbol itself