Add new method for dumping data from read_coverage table

Data is dumped from table and written in fasta format as
remapping input
Write method for dumping read coverage data
Write method for generating fasta files for read data dumped from
read coverage table
Add method for filtering read coverage mapping results
Initialise file names in a loop
Initialise file names with individual id

This is needed when running in remap_read_coverage mode
Add option to filter read coverage mapping results
Add method for filtering read coverage mapping results
Replace generate_fasta_files with use_fasta_files

Default value for use_fasta_files is 0. Only if fasta files
have been generate you can set it to 1.
Check fasta files exist if option use_fasta_files is set
Delete fasta index files
Remove check if bam_files dir is empty

Bam_files dir is newly generated.
Bug fix
Bug fix
Bug fix
Bug fix
Bug fix
Bug fix
Bug fix
Merge branch 'master' of https://github.com/Ensembl/ensembl-variation