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Require at least two occurrences in the base sequence when making com…

…parative calls
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commit ef79e9e603d08cc78414d3e62cafaf241f624458 1 parent 20519aa
@jts authored
Showing with 2 additions and 1 deletion.
  1. +2 −1  src/GraphDiff/GraphCompare.cpp
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3  src/GraphDiff/GraphCompare.cpp
@@ -146,6 +146,7 @@ GraphCompareResult GraphCompare::process(const SequenceWorkItem& item)
count += rc_interval.size();
bool both_strands = interval.size() > 0 && rc_interval.size() > 0;
+ size_t min_base_coverage = m_parameters.bReferenceMode ? 1 : 2;
if(count >= m_parameters.minDiscoveryCount && count < m_parameters.maxDiscoveryCount && !variantAttempted && both_strands)
{
@@ -153,7 +154,7 @@ GraphCompareResult GraphCompare::process(const SequenceWorkItem& item)
size_t base_count = BWTAlgorithms::countSequenceOccurrences(kmer, m_parameters.baseIndex);
// k-mer present in the base read set, skip it
- if(base_count > 0)
+ if(base_count >= min_base_coverage)
continue;
if(m_parameters.verbose > 0)
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