libsequence  1.9.5
allele_counts.hpp
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1 #ifndef SEQUENCE_SUMMSTATS_ALLELE_COUNTS_HPP__
4 #define SEQUENCE_SUMMSTATS_ALLELE_COUNTS_HPP__
5 
6 #include <vector>
7 #include <utility>
8 #include <cstdint>
9 #include <Sequence/AlleleCountMatrix.hpp>
10 
11 namespace Sequence
12 {
13  struct AlleleCounts
16  {
18  int nstates;
20  int nmissing;
21  };
22 
27  std::vector<AlleleCounts> allele_counts(const AlleleCountMatrix& m);
28 
34  std::vector<AlleleCounts>
35  non_reference_allele_counts(const AlleleCountMatrix& m,
36  const std::int8_t refstate);
37 
43  std::vector<AlleleCounts>
44  non_reference_allele_counts(const AlleleCountMatrix& m,
45  const std::vector<std::int8_t>& refstates);
46 } // namespace Sequence
47 #endif
Sequence::allele_counts
std::vector< AlleleCounts > allele_counts(const AlleleCountMatrix &m)
Count number of alleles at each site.
Definition: allele_counts.cc:50
Sequence::AlleleCounts::nstates
int nstates
Number of non-missing states.
Definition: allele_counts.hpp:18
Sequence
The namespace in which this library resides.
Sequence::AlleleCounts::nmissing
int nmissing
Number of samples with missing states.
Definition: allele_counts.hpp:20
Sequence::AlleleCountMatrix
Matrix representation of allele counts in a VariantMatrix To be constructed.
Definition: AlleleCountMatrix.hpp:12
Sequence::non_reference_allele_counts
std::vector< AlleleCounts > non_reference_allele_counts(const AlleleCountMatrix &m, const std::int8_t refstate)
Count number of non-reference alleles at each site.
Definition: allele_counts.cc:80