do not run unique_modus it is quite inefficient

cbg-ethz · Jan 30, 2024 · 93db921 · 93db921
1 parent 98005e3
commit 93db921
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/viloca/local_haplotype_inference/learn_error_params/run_dpm_mfa.py b/viloca/local_haplotype_inference/learn_error_params/run_dpm_mfa.py
@@ -29,7 +29,7 @@ def gzip_file(f_name):
     return f_out.name
 
 
-def main(freads_in, fref_in, output_dir, n_starts, K, alpha0, alphabet="ACGT-", unique_modus=True):
+def main(freads_in, fref_in, output_dir, n_starts, K, alpha0, alphabet="ACGT-", unique_modus=False):
 
     window_id = freads_in.split("/")[-1][:-4]  # freads_in is absolute path
 
@@ -39,7 +39,7 @@ def main(freads_in, fref_in, output_dir, n_starts, K, alpha0, alphabet="ACGT-",
     # Read in reads
     reference_seq, ref_id = preparation.load_reference_seq(fref_in)
     reference_binary = preparation.reference2binary(reference_seq, alphabet)
-    reads_list = preparation.load_fasta2reads_list(freads_in, alphabet, unique_modus)
+    reads_list = preparation.load_fasta2reads_list(freads_in, alphabet, False)
     reads_seq_binary, reads_weights = preparation.reads_list_to_array(reads_list)
 
     if n_starts >1:

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
@@ -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(