standard option names added

Comment changes.

UCSC.

the add_xref() method for coordinate-based Xrefs.

Based on the knownGenes table from UCSC.

added get_all_Genes_by_source and made get_all_Genes_by type select at teh sql level rather than later on using grep

  Note in the POD that the new $no_fuzz argument is optional and by
  default undef (false).

  Sorted out possible SQL precedence problem (idea from James).

  Old SQL (fragment):

    FROM (transcript t)
      LEFT JOIN transcript_stable_id tsi
        ON tsi.transcript_id = t.transcript_id
      LEFT JOIN xref x
        ON x.xref_id = t.display_xref_id
      LEFT JOIN external_db exdb
        ON exdb.external_db_id = x.external_db_id

  New SQL (same fragment):

    FROM
      ( ( ( (transcript t)
            LEFT JOIN transcript_stable_id tsi
              ON tsi.transcript_id = t.transcript_id
          )
          LEFT JOIN xref x
            ON x.xref_id = t.display_xref_id
        )
        LEFT JOIN external_db exdb
          ON exdb.external_db_id = x.external_db_id
      )

    Arg [7]    : boolean $no_fuzz
                 If true, do not use "fuzzy matching" (see below).

  This was done to allow the user to by-pass the fuzzy matching code.
  This will allow for some speed increases and to remove any ambiguity
  around the results from this method.

  Also inserted clarifying comment about stickleback DB ('groups' vs.
  'chromosomes') from Anne.

sequence returnes by seq call returns the number of bases specified by the length of the StrainSlice

the coding region does not start/end in this exon, it also will not
end/start here.

host added for pre-sites

options standardised

Small change to build_transcript_and_gene_display_xrefs subroutine so that gene get their own display_xref instead of being assigned one from a transcript.

Made pattern matching more strict when choosing type (gene, transcript, translation) as 'pseudogene' transcripts had previously been classified as genes.