add minimum number of iterations

cbg-ethz · Nov 26, 2024 · 987ab13 · 987ab13
1 parent 8dc0545
commit 987ab13
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/viloca/local_haplotype_inference/use_quality_scores/analyze_results.py b/viloca/local_haplotype_inference/use_quality_scores/analyze_results.py
@@ -31,7 +31,7 @@ def haplotypes_to_fasta(state_curr_dict, output_dir):
         ave_reads = state_curr_dict["weight" + str(k)]
         if ave_reads==0:
             # this haplotype will not be reported as there are no reads
-            # supporting it. 
+            # supporting it.
             continue
 
         head = (

diff --git a/viloca/local_haplotype_inference/use_quality_scores/cavi.py b/viloca/local_haplotype_inference/use_quality_scores/cavi.py
@@ -114,8 +114,9 @@ def run_cavi(
     iter = 0
     converged = False
     elbo = 0
+    min_number_iterations = 10
     state_curr_dict = state_init_dict
-    while converged is False:
+    while (converged is False) or (iter < min_number_iterations):
 
         if iter <= 1:
             digamma_alpha_sum = digamma(state_curr_dict["alpha"].sum(axis=0))
@@ -155,7 +156,7 @@ def run_cavi(
                 break
             elif (history_elbo[-2] > elbo) and np.abs(elbo - history_elbo[-2]) > 1e-08:
                 exit_message = "Error: ELBO is decreasing."
-                break
+                #break
             elif np.abs(elbo - history_elbo[-2]) < convergence_threshold:
                 converged = True
                 exit_message = "ELBO converged."