Merge branch 'mmaiers-nmdp-absolutepaths'

Author: pbashyal-nmdp

.github/PULL_REQUEST_TEMPLATE/pull_request_template.md

@@ -3,6 +3,6 @@ Description of Pull Request..
 ## Checklist
 
 - [ ] Unit tests
-- [ ] Documentation 
+- [ ] Documentation
 
 Fixes #

.gitignore

@@ -139,4 +139,5 @@ allure_report/
 # cython temp files
 grim/**/*.c
 
+.DS_Store
 output/

conf/minimal-configuration.json

@@ -51,5 +51,5 @@
   "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
 
@@ -205,7 +206,10 @@ def loci_order(loc_values):
 
 
 def generate_graph(
-    config_file="../conf/minimal-configuration-script.json", em_pop=None, em=False, use_default_path = False
+    config_file="../conf/minimal-configuration-script.json",
+    em_pop=None,
+    em=False,
+    use_default_path=False,
 ):
     ##############################################################################
     # Configure
@@ -217,7 +221,7 @@ def generate_graph(
     # freq_file = path  + freq_file
     path = ""
     if use_default_path:
-         path =  os.path.dirname(os.path.realpath(__file__)) + "/"
+        path = os.path.dirname(os.path.realpath(__file__)) + "/"
     parser = argparse.ArgumentParser()
     parser.add_argument(
         "-c",