text: # Programs
  trimmomatic_jar = "/data/reddylab/software/Trimmomatic-0.32/trimmomatic-0.32.jar"
  picard_jar = "/data/reddylab/software/picard/dist/picard.jar"
  
  # Auxiliary reference files (species agnostic)
  as_narrowPeak = '/data/reddylab/Reference_Data/ENCODE/kent/src/hg/lib/encode/narrowPeak.as'
  as_broadPeak = '/data/reddylab/Reference_Data/ENCODE/kent/src/hg/lib/encode/broadPeak.as'
  
  class ReferenceDataset(object):
      def __init__(self, genome='hg38'):
          self.default_adapters = "/data/reddylab/projects/GGR/auxiliary/adapters/default_adapters.fasta"
          _genome = genome.lower()
          if _genome == 'hg38' or _genome == 'grch38':
              self.bowtie_genome_ref_first_index = "/data/reddylab/Reference_Data/Genomes/hg38/GCA_000001405.15_GRCh38_no_alt_analysis_set.1.ebwt"
              self.star_genome_dir = "/data/reddylab/Reference_Data/Genomes/hg38/STAR_genome_sjdbOverhang_49_novelSJDB"
              self.genome_sizes_file = "/data/reddylab/projects/GGR/auxiliary/hg38.sizes"
              self.encode_blacklist_bedfile = "/data/reddylab/Reference_Data/ENCODE/hg38.blacklist.bed"
              self.genome_effective_size = "hs"
          elif _genome == 'hg19' or _genome == 'grch37':
              self.bowtie_genome_ref_first_index = "/data/reddylab/Reference_Data/Genomes/hg19/hg19.1.ebwt"
              self.star_genome_dir = "/data/reddylab/Reference_Data/Genomes/hg19/STAR_genome_sjdbOverhang_50"
              self.genome_sizes_file = "/data/reddylab/Reference_Data/Genomes/hg19/hg19.chrom.sizes"
              self.encode_blacklist_bedfile = "/data/reddylab/Reference_Data/ENCODE/wgEncodeDacMapabilityConsensusExcludable.hg19.bed"
              self.genome_effective_size = "hs"
          elif _genome == 'mm10' or _genome == 'grcm38':
              self.bowtie_genome_ref_first_index = "/data/reddylab/Reference_Data/Genomes/mm10/bowtie/GRCm38.1.ebwt"
              self.star_genome_dir = "/data/reddylab/Reference_Data/Genomes/mm10/STAR_genome_sjdbOverhang_49_novelSJDB"
              self.genome_sizes_file = "/data/reddylab/Reference_Data/Genomes/GRCm38/GRCm38.sizes"
              self.encode_blacklist_bedfile = "/data/reddylab/Reference_Data/ENCODE/mm10.blacklist.bed"
              self.genome_effective_size = "mm"
          elif _genome == 'mm9' or _genome == 'ncbi37':
              self.bowtie_genome_ref_first_index = "/data/reddylab/Reference_Data/Genomes/mm9/bowtie/mm9.1.ebwt"
              self.star_genome_dir = "/data/reddylab/Reference_Data/Genomes/mm9/STAR_genome_sjdbOverhang_50_novelSJDB"
              self.genome_sizes_file = "/data/reddylab/Reference_Data/Genomes/mm9/mm9.chrom.sizes"
              self.encode_blacklist_bedfile = "/data/reddylab/Reference_Data/ENCODE/mm9.blacklist.bed"
              self.genome_effective_size = "mm"
          elif _genome == 'danrer10' or _genome == 'grcz10':
              self.bowtie_genome_ref_first_index = "/data/reddylab/Reference_Data/Genomes/danRer10/bowtie/danRer10.1.ebwt"
              self.star_genome_dir = "/data/reddylab/Reference_Data/Genomes/danRer10/STAR_genome_sjdbOverhang_50_novelSJDB"
              self.genome_sizes_file = "/data/reddylab/Reference_Data/Genomes/danRer10/danRer10.chrom.sizes"
              self.encode_blacklist_bedfile = None
              self.genome_effective_size = "1.04e9"
          else:
              raise Exception("Genome %s not recognized" % genome)
  