add support for absolute paths and fix typo in default config

Author: mmaiers-nmdp

conf/minimal-configuration.json

@@ -52,5 +52,5 @@
   "imputation_out_miss_filename": "don.miss",
   "imputation_out_problem_filename": "don.problem",
   "max_haplotypes_number_in_phase": 100,
-  "imuptation_out_path": "output"
+  "imputation_out_path": "output"
 }

graph_generation/generate_hpf.py

@@ -4,7 +4,7 @@
 import pathlib
 import argparse
 
-project_dir = "./"
+project_dir = ""
 
 parser = argparse.ArgumentParser()
 parser.add_argument(
@@ -32,7 +32,7 @@
 
 
 # Create output directory if it doesn't exist
-pathlib.Path(output_dir).mkdir(parents=False, exist_ok=True)
+pathlib.Path(output_dir).mkdir(parents=True, exist_ok=True)
 
 # Display the configurations we are using
 print(

graph_generation/generate_neo4j_multi_hpf.py

@@ -62,6 +62,7 @@ def make_allele_list(haplotype, full_name_index_dict, num_of_alleles):
     sorted_h1 = ["0"] * num_of_alleles
     for allele in hl:
         locus = allele.split("*")[0]
+        # print(allele, hl)
         sorted_h1[full_name_index_dict[locus] - 1] = allele
     return sorted_h1