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std::pair< char, double > | consensus (BaseCounts const &sample) |
| Consensus character for a BaseCounts, and its confidence. More...
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std::pair< char, double > | consensus (BaseCounts const &sample, BaseCountsStatus const &status) |
| Consensus character for a BaseCounts, and its confidence. More...
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size_t | get_base_count (BaseCounts const &bc, char base) |
| Get the count for a base given as a char. More...
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char | guess_alternative_base (Variant const &variant, bool force=true) |
| Guess the alternative base of a Variant. More...
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char | guess_reference_base (Variant const &variant) |
| Guess the reference base of a Variant. More...
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BaseCounts | merge (BaseCounts const &p1, BaseCounts const &p2) |
| Merge the counts of two BaseCountss. More...
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BaseCounts | merge (std::vector< BaseCounts > const &p) |
| Merge the counts of a vector BaseCountss. More...
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void | merge_inplace (BaseCounts &p1, BaseCounts const &p2) |
| Merge the counts of two BaseCountss, by adding the counts of the second (p2 ) to the first (p1 ). More...
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template<typename T > |
std::array< size_t, 4 > | nucleotide_sorting_order_ (std::array< T, 4 > const &values) |
| Local helper function that runs a sorting network to sort four values, coming from the four nucleotides. More...
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std::ostream & | operator<< (std::ostream &os, BaseCounts const &bs) |
| Output stream operator for BaseCounts instances. More...
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std::pair< SortedBaseCounts, SortedBaseCounts > | sorted_average_base_counts (BaseCounts const &sample_a, BaseCounts const &sample_b) |
| Return the sorted base counts of both input samples, orderd by the average frequencies of the nucleotide counts in the two samples. More...
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SortedBaseCounts | sorted_base_counts (BaseCounts const &sample) |
| Return the order of base counts (nucleotides), largest one first. More...
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SortedBaseCounts | sorted_base_counts (Variant const &variant, bool reference_first) |
| Get a list of bases sorted by their counts. More...
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BaseCountsStatus | status (BaseCounts const &sample, size_t min_coverage=0, size_t max_coverage=0, size_t min_count=0, bool tolerate_deletions=false) |
| Compute a simple status with useful properties from the counts of a BaseCounts. More...
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BaseCounts | total_base_counts (Variant const &variant) |
| Get the summed up total base counts of a Variant. More...
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