Merge pull request #27 from CenterForMedicalGeneticsGhent/gonosome_ma…

…sking Made gonosome masking equally stringent between male/female
CenterForMedicalGeneticsGhent · Jan 17, 2019 · 3ca00e1 · 3ca00e1
2 parents 5c941f4 + f7a6503
commit 3ca00e1
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/wisecondorX/predict_control.py b/wisecondorX/predict_control.py
@@ -25,7 +25,7 @@ def normalize(args, sample, ref_file, ref_gender):
     sample = coverage_normalize_and_mask(sample, ref_file, ap)
     sample = project_pc(sample, ref_file, ap)
     results_w = get_weights(ref_file, ap)[ct:]
-    optimal_cutoff = get_optimal_cutoff(ref_file, args.maskrepeats, ct, ap)
+    optimal_cutoff = get_optimal_cutoff(ref_file, args.maskrepeats)
     results_z, results_r, ref_sizes, m_lr, m_z = normalize_repeat(sample, ref_file, optimal_cutoff, ct, cp, ap)
 
     return results_r, results_z, results_w, ref_sizes, m_lr, m_z

diff --git a/wisecondorX/predict_tools.py b/wisecondorX/predict_tools.py
@@ -67,8 +67,8 @@ def project_pc(sample_data, ref_file, ap):
 '''
 
 
-def get_optimal_cutoff(ref_file, repeats, ct, ap):
-    distances = ref_file['distances{}'.format(ap)][ct:]
+def get_optimal_cutoff(ref_file, repeats):
+    distances = ref_file['distances']
     cutoff = float('inf')
     for i in range(0, repeats):
         mask = distances < cutoff