Support for multiple contigs and summary calculations

Added

• Full support for genomes with multiple contigs/chromosomes (#5)
• Full support of masking regions of the genome from analysis (#11)
• Full support for normalization based on a known background region (#6)
• Calculate summaries over regions or locations (#14)
• Ability to specify parameter strings for certain rules either as a single
  value for every sample or through specifying a column in the metadata sheet
  for by sample control
• Ability to add pseudocount before within sample normalization. Only implemented for median normalization
• Support for normalization based on averages over a given set of regions.
  Enables Occupancy Apparent calculations.
• Support for normalization for occupancy apparent calculations by dynamically
  determining the highest and lowest N genes by average signal
• Support for reciprocal ratio calculations to keep ratios in a linear scale.
  Inverts all ratios less than one and takes negative value. Then subtracts or
  adds 1 to recenter to zero.
• Added a specification to exclude Infs and NaNs from bigwig files

Changed

• Config syntax change for specifying genome inputs
• Removed general pseudocount specification. Never adds a pseudocount for ratios
• Substantially updated the bwtools.py module to enable summary calculations
• Config syntax change for coverage and normalization specification

Bug fixes

• Fixed an issue when running coverage_and_norm module only (#3)
• Fixed an issue with the tbb version being too high on some systems causing bowtie2 to fail to run (workflow/envs/alignment.yaml file).
• Fixed an issue where genome size was not properly read as input to Macs2 in workflow/rules/peak_calling.smk
• Fixed an issue where filename paths with spaces in them would not input correctly to cutadapt workflow/rules/preprocessing.smk