Prepend database directory path on to relative paths for allele fasta…

… files in db

src/calling_functions.jl

@@ -11,11 +11,15 @@ function run_calling_pipeline(args)
 
   # check if DB and fastq files exist:
   check_files([args["db"];[fastq for fq_files in values(sample_files) for fastq in fq_files]])
+  db_path = dirname(args["db"])
   # array for saving each sample result:
   sample_results = []
   info("Opening kmer database ... ")
   kmer_db, loci, loci2alleles, k, profile, build_args = open_db(args["db"])
-
+  # prepend base path of the kmer database on to the relative paths for allele fasta files stored in the db
+  for (index, file) in enumerate(build_args["fasta_files"])
+    build_args["fasta_files"][index] = dirname(args["db"]) * "/" * file
+  end
   # process each sample:
   for (sample, fq_files) in sample_files
     info("Sample: $sample. Opening fastq file(s) and counting kmers ... ")