From f6cdaa2046aac1145bc15c5b062bded85a51b124 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Tue, 26 Nov 2024 09:16:59 +0100
Subject: [PATCH] Revert "Merge pull request #38 from
 cbg-ethz/enable-unique-modus"

This reverts commit ffd4fd13575b9412fda3d689e5b3b588dc1587ef, reversing
changes made to 279cc634a5d7856b9b280aef5b29a7b647d97407.
---
 .../use_quality_scores/analyze_results.py              |  2 +-
 .../use_quality_scores/cavi.py                         |  5 ++---
 .../use_quality_scores/run_dpm_mfa.py                  | 10 +++++-----
 3 files changed, 8 insertions(+), 9 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 4093ff2..ed0a6b2 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 bfce3d9..3ff3c58 100644
--- a/viloca/local_haplotype_inference/use_quality_scores/cavi.py
+++ b/viloca/local_haplotype_inference/use_quality_scores/cavi.py
@@ -114,9 +114,8 @@ def run_cavi(
     iter = 0
     converged = False
     elbo = 0
-    min_number_iterations = 10
     state_curr_dict = state_init_dict
-    while (converged is False) or (iter < min_number_iterations):
+    while converged is False:
 
         if iter <= 1:
             digamma_alpha_sum = digamma(state_curr_dict["alpha"].sum(axis=0))
@@ -156,7 +155,7 @@ 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."
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 b534c00..58ff5b4 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=True,
+    unique_modus=False,
     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, unique_modus
+        freads_in, fname_qualities, alphabet, False
     )
     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],
-        sys.argv[4],
+        int(sys.argv[4]),
         int(sys.argv[5]),
-        int(sys.argv[6]),
-        float(sys.argv[7]),
+        float(sys.argv[6]),
+        sys.argv[7],
     )
 # freads_in, fref_in, output_dir, n_starts, K, alpha0, alphabet = 'ACGT-'