From 7ced8b8330259f057e624f364f9db8db79c36603 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Sun, 10 Nov 2024 16:51:41 +0100
Subject: [PATCH 1/2] add minimum number of iterations

---
 .../use_quality_scores/analyze_results.py                    | 2 +-
 viloca/local_haplotype_inference/use_quality_scores/cavi.py  | 5 +++--
 2 files changed, 4 insertions(+), 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
index ed0a6b2..4093ff2 100644
--- 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
index 3ff3c58..bfce3d9 100644
--- 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."

From 822f341890f390ad7e856a56988b70e7c60120ca Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Sun, 10 Nov 2024 16:52:13 +0100
Subject: [PATCH 2/2] pass unique_modus argument

---
 .../use_quality_scores/run_dpm_mfa.py                  | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/viloca/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py b/viloca/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py
index b62a84f..eb0c692 100644
--- a/viloca/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py
+++ b/viloca/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py
@@ -33,7 +33,7 @@ def main(
     K,
     alpha0,
     alphabet="ACGT-",
-    unique_modus=False,
+    unique_modus=True,
     convergence_threshold=1e-03,
 ):
 
@@ -46,7 +46,7 @@ def main(
     reference_binary, ref_id = preparation.load_reference_seq(fref_in, alphabet)
 
     reads_list, qualities = preparation.load_fasta_and_qualities(
-        freads_in, fname_qualities, alphabet, False
+        freads_in, fname_qualities, alphabet, unique_modus
     )
     reads_seq_binary, reads_weights = preparation.reads_list_to_array(reads_list)
     reads_log_error_proba = preparation.compute_reads_log_error_proba(
@@ -147,9 +147,9 @@ def main(
         sys.argv[1],
         sys.argv[2],
         sys.argv[3],
-        int(sys.argv[4]),
+        sys.argv[4],
         int(sys.argv[5]),
-        float(sys.argv[6]),
-        sys.argv[7],
+        int(sys.argv[6]),
+        float(sys.argv[7]),
     )
 # freads_in, fref_in, output_dir, n_starts, K, alpha0, alphabet = 'ACGT-'