old_contents: #! /usr/bin/env python
  
  """
  
  Copyright [1999-2018] EMBL-European Bioinformatics Institute
  
  Licensed under the Apache License, Version 2.0 (the "License")
  you may not use this file except in compliance with the License.
  You may obtain a copy of the License at
  
  		 http://www.apache.org/licenses/LICENSE-2.0
  
  Unless required by applicable law or agreed to in writing, software
  distributed under the License is distributed on an "AS IS" BASIS,
  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  See the License for the specific language governing permissions and
  limitations under the License.
  
  """
  
  """
  
  	Please email comments or questions to the public Ensembl
  	developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
  
  	Questions may also be sent to the Ensembl help desk at
  	<http://www.ensembl.org/Help/Contact>.
  
  """
  from postgap.DataModel import Region
  
  DATABASES_DIR = None
  SPECIES = None
  DEBUG = True
  
  BLACKLISTED_REGIONS = [
  	Region(chrom = '6', start=28477797, end=33448354), # MHC
  	Region(chrom = '17', start=44165260, end=44784489) # Dan Wright's inversion
  ]
  
  EVIDENCE_WEIGHTS = {
  	'Regulome': 1,
  	'VEP': 1,
  	'GTEx': 1,
  	'Fantom5': 1,
  	'DHS': 1,
  	'PCHiC': 1,
  	'Nearest': 1
  }
  
  GWAS_adaptors = None
  Cisreg_adaptors = None
  Reg_adaptors = None
  
  GTEx_path = None
  SQLite_connection = None
  work_directory = "notset"
  finemap_gwas_clusters_directory = None
  
  GWAS_PVALUE_CUTOFF = 1e-4
  
  GWAS_SUMMARY_STATS_FILE = None
  
  PERFORM_BAYESIAN = False
  
  ALL_TISSUES=[]
  
new_contents: #! /usr/bin/env python
  
  """
  
  Copyright [1999-2018] EMBL-European Bioinformatics Institute
  
  Licensed under the Apache License, Version 2.0 (the "License")
  you may not use this file except in compliance with the License.
  You may obtain a copy of the License at
  
  		 http://www.apache.org/licenses/LICENSE-2.0
  
  Unless required by applicable law or agreed to in writing, software
  distributed under the License is distributed on an "AS IS" BASIS,
  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  See the License for the specific language governing permissions and
  limitations under the License.
  
  """
  
  """
  
  	Please email comments or questions to the public Ensembl
  	developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
  
  	Questions may also be sent to the Ensembl help desk at
  	<http://www.ensembl.org/Help/Contact>.
  
  """
  from postgap.DataModel import Region
  
  DATABASES_DIR = None
  SPECIES = None
  DEBUG = False
  
  BLACKLISTED_REGIONS = [
  	Region(chrom = '6', start=28477797, end=33448354), # MHC
  	Region(chrom = '17', start=44165260, end=44784489) # Dan Wright's inversion
  ]
  
  EVIDENCE_WEIGHTS = {
  	'Regulome': 1,
  	'VEP': 1,
  	'GTEx': 1,
  	'Fantom5': 1,
  	'DHS': 1,
  	'PCHiC': 1,
  	'Nearest': 1
  }
  
  GWAS_adaptors = None
  Cisreg_adaptors = None
  Reg_adaptors = None
  
  GTEx_path = None
  SQLite_connection = None
  work_directory = "notset"
  finemap_gwas_clusters_directory = None
  
  GWAS_PVALUE_CUTOFF = 1e-4
  
  GWAS_SUMMARY_STATS_FILE = None
  
  PERFORM_BAYESIAN = False
  
  ALL_TISSUES=[]
  
subject: Debug mode now optional