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Allow the use of --limit sequences when clustering reads

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commit c870b44ec68306bc63bce496da69b2cc2bc6036a 1 parent 7cb3e10
@jts authored
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4 src/Algorithm/ClusterProcess.cpp
@@ -42,6 +42,10 @@ ClusterResult ClusterProcess::process(const SequenceWorkItem& item)
}
}
+ // Add sequences to be used to stop extension, if requested
+ if(m_parameters.pLimitKmers != NULL)
+ cluster.setLimitKmers(m_parameters.pLimitKmers, m_parameters.limitK);
+
// Run the clustering process
cluster.run(m_parameters.maxClusterSize, 0);
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3  src/Algorithm/ReadCluster.cpp
@@ -115,7 +115,7 @@ void ReadCluster::run(size_t max_size, int max_iterations)
// Add this node to the output
m_outCluster.push_back(node);
-
+
// If we are using limit kmers, only try to extend this sequence if it does not contain a limit kmer
bool extend_read = canExtendRead(node);
if(!extend_read)
@@ -171,7 +171,6 @@ bool ReadCluster::canExtendRead(const ClusterNode& node) const
// No limiting kmers
if(m_pLimitKmers == NULL)
return true;
-
// Node too short
if(node.sequence.size() < m_limitK)
return false;
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