Commit 8d50dc49 authored by Jan Hoeckesfeld's avatar Jan Hoeckesfeld
Browse files

added faulty spatypes error message

parent de710308
/data/*
config.yaml
.snakemake/
.idea/*
__pycache__/
benchmarks/
logs/
report/
\ No newline at end of file
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......@@ -28,16 +28,16 @@ assembly_model : False
###Reference Genome
reference_genome : NCTC8325
genome_file_identifier : genome.fa #NCTC8325
#genome_file_identifier : genome.fna
protein_table_identifier : protein.table
# genome_file_identifier : genome.fna # Found here: https://www.ncbi.nlm.nih.gov/assembly/GCF_900475245.1
protein_table_identifier : protein.table # "feature table"
reference_guided_assembly : False
# reference_genome_table refers to protein_table!
reference_genome_table_index_organism_id : 6 #NCTC8325
reference_genome_table_index_start_pos : 7 #H-EMRSA-15 #NCTC8325
reference_genome_table_index_end_pos : 8 #H-EMRSA-15 #NCTC8325
reference_genome_table_index_strand : 9 #H-EMRSA-15 #NCTC8325
reference_genome_table_index_protein_id : 13 #H-EMRSA-15 #NCTC8325
reference_genome_table_index_strand : 9 #H-EMRSA-15 #NCTC8325 # + or -
reference_genome_table_index_protein_id : 13 #H-EMRSA-15 #NCTC8325 # where the protein_a_identifier is located!
protein_a_identifier : protein A #NCTC8325
l_lactate_permease_identifier : L-lactate permease #NCTC8325
......@@ -81,7 +81,7 @@ dps : 100
#countMean -> k-mer coverage is based on a k-mer frequency histogram where the average k-mer coverage is estimated by the mean of k-mer frequencies (again, cutting off error k-mers)
kmerCoverageEstimationMethod : countPoisson
#when calclating probabilities based on COV method, skip a tpye as soon as the deviation between expected and observed exceeds (deviationCutoff*kmerCoverageEstimate) for any k-mer
#when calculating probabilities based on COV method, skip a type as soon as the deviation between expected and observed exceeds (deviationCutoff*kmerCoverageEstimate) for any k-mer
deviationCutoff : 2.5
#likelihoods exceeding this value are not taken into account when calculating a prior
#likelihoodCutoff : -50000
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