added faulty spatypes error message

.gitignore

+/data/*
+config.yaml
+.snakemake/
+.idea/*
+__pycache__/
+benchmarks/
+logs/
+report/
\ No newline at end of file

config.example.yaml

@@ -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