From b7851b428e692bf202a9649dd83b468b539d0052 Mon Sep 17 00:00:00 2001
From: oboulle <olivier.boulle@inria.fr>
Date: Mon, 4 Dec 2023 17:15:15 +0100
Subject: [PATCH] remove consensus limit and dumping
---
reads_consensus_class.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/reads_consensus_class.py b/reads_consensus_class.py
index a028e8c..2a597cc 100755
--- a/reads_consensus_class.py
+++ b/reads_consensus_class.py
@@ -65,8 +65,8 @@ def consensus_class_init(kmer_occ_dict: dict, kmer_size: int, start_primer: str,
start_kmer_score_occ = Consensus.kmer_occurrences_dict[start_kmer]
Consensus.list_of_consensus_to_explore.append([start_kmer_score_occ, "start", 0, start_kmer])
- # continue to explore new consensus, but stop at 10 000 consensus (arbitrary)
- while Consensus.list_of_consensus_to_explore != [] and Consensus.consensus_number <= 10000:
+ # continue to explore new consensus
+ while Consensus.list_of_consensus_to_explore:# and Consensus.consensus_number <= 30000:
[score, father_name, split_index, start_kmer] = Consensus.list_of_consensus_to_explore.pop() # get last element # the one with higher score
create_new_consensus(father_name, split_index, start_kmer) # run the new consensus
@@ -597,7 +597,7 @@ def kmer_consensus(input_path: str, output_path: str, start_primer: str, stop_pr
#print("paths creation " +str(round(consensus_time, 3)))
start = time.time()
# remove the consensus of len <= kmer size, because they are created only out of 1 error on a kmer
- dump_short_consensus()
+ #dump_short_consensus()
dumping_time = time.time() - start
#print("dump paths "+str(round(dumping_time, 3)))
--
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