Warn is assembly_exception table is empty.

  there's no need to start the index at '1'.
* Don't check the assembly_exception table if this is the first set of
  patches to be added.

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).

Temporary fix to solve incorrect orientation of the HG1211_PATCH until either the file contains this information or we decide to do it another way

Modified to deal with alt_scaffold_placement.txt ori=b, to process the files from GRC (skipping previously loaded patches) and load the patches into the supercontig level of the assembly (as well as chromosome and contig) along with the chrom-supercontig and supercontig-chrom mappings.

calculations, implemented by Steve Searle.

Get sequence using mfetch as fasta file has fasta of the pathced region and not of the contigs that make up this region