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mapgd
0.4
A program for the Maximum-likelihood analysis of population genomic data.
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mapgd
0.4
A program for the Maximum-likelihood analysis of population genomic data.
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Public Member Functions | |
| void | write_binary (std::ostream &out) const |
| void | read_binary (std::istream &in) |
| Locus (const count_t &) | |
| Locus is initialized to abs_pos_=0, id1=0, and set to contain 0 samples. | |
| Locus () | |
| Locus is initialized to abs_pos_=0, id1=0, and set to contain 0 samples. | |
| Locus (const std::vector< std::string > &) | |
| Locus & | operator= (const Locus &) |
| Locus & | operator+= (const Locus &) |
| const Locus | operator+ (const Locus &) const |
| const count_t | getindex (count_t) const |
| Returns the index of the alleles in order a sorted order. More... | |
| count_t | getcoverage (count_t) const |
| Returns coverage of population/individual N. | |
| count_t | getcoverage (void) const |
| Returns total coverage. | |
| count_t | getcount (count_t) const |
| Returns the count of allele in all individuals in the population. | |
| count_t | getcount (count_t, count_t) const |
| Returns the count of individual a's b'th allele. | |
| void | swap (count_t, count_t) |
| Exchange the alleles. | |
| void | sort (count_t) |
| Sort counts from most common to least common (based on population N). | |
| void | sort (void) |
| Sort counts from most common to least common (among all non-masked sites). | |
| void | set_quartet (const quartet_t &, const count_t &) |
| Sets the quartet_t array (unsorted). More... | |
| const quartet_t & | get_quartet (const count_t &) const |
| Returns the N'th quartet at the Locus. More... | |
| quartet_t & | get_quartet (const count_t &) |
| Returns the N'th quartet at the Locus. More... | |
| count_t | maskedcount (void) const |
| Returns the count of the number of individuals that are masked. | |
| void | maskall (void) |
| Mask all lines. More... | |
| void | unmaskall (void) |
| Unmask all lines. More... | |
| void | mask (const std::vector< size_t > &) |
| Mask all lines. More... | |
| void | unmask (const std::vector< size_t > &) |
| Unmask all lines. More... | |
| void | mask_low_cov (const count_t &dp) |
| Mask site with coverage stricktly lt dp;. | |
| char | getname (const count_t &) const |
| Get the nucleotide represented by the count at the N'th indexed quartet_t. | |
| char | getname_gt (const count_t &) const |
| Get the nucleotide represented by the count at the N'th indexed quartet_t, return * if the count equals the N+1 indexed quartet. | |
| count_t | get_extraid (const size_t &) const |
| Get the extraid of the Locus. Used to represent the reference call. | |
| void | set_extraid (const count_t &, const size_t &) |
| Set the extraid of the Locus. Just used to represent the reference call. | |
| void | resize (const size_t &) |
| < Set the absolute position of the Locus. More... | |
| std::vector< quartet_t >::iterator | begin (void) |
| std::vector< quartet_t >::iterator | end (void) |
| Return an iterator to the quartet_t s stored at this Locus. More... | |
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std::vector< quartet_t > ::const_iterator | cbegin (void) const |
| Return an iterator to the quartet_t s stored at this Locus. | |
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std::vector< quartet_t > ::const_iterator | cend (void) const |
| Return an iterator to the quartet_t s stored at this Locus. | |
| std::vector< std::string > | get_sample_names (void) const |
| names of the samples sequenced | |
| void | set_sample_names (const std::vector< std::string > &sample_names) |
| names of the samples sequenced. | |
| std::string | header (void) const |
| size_t | size (void) const |
| The size of the class in bytes. | |
| const std::string | get_file_name (void) const |
| const std::string | get_table_name (void) const |
| const bool | get_binary (void) const |
| const std::string | sql_header (void) const |
| Return the names of the columns, along with variable type. | |
| const std::string | sql_column_names (void) const |
| Return the names of the columns. | |
| const std::string | sql_values (void) const |
| Return the values to be placed in columns. | |
| void | sql_read (std::istream &) override |
| Reads the values... | |
 Public Member Functions inherited from Indexed_data | |
| void | write_pos (std::ostream &str) const |
| void | read_pos (std::istream &str) |
| Indexed_data (std::vector< std::string > &) | |
| id1_t | get_abs_pos (void) const |
| Indexed data needs to associate each datum with a position in the genome. | |
| void | set_abs_pos (const id1_t &) |
| Indexed data needs to associate each datum with a position in the genome. | |
| const bool | indexed () const |
| Public Member Functions inherited from Data | |
| void | read_binary (std::istream &str) |
| void | write_binary (std::ostream &str) const |
| Data (std::vector< std::string > &) | |
Data Fields | |
| gt_t | sorted_ [5] |
| an array to allow sorted access to quartets. | |
| std::vector< quartet_t > | sample |
| The five bases A/C/G/T/N;. | |
| Base | ref |
Static Public Attributes | |
| static const gt_t | default_order [5] = {0,1,2,3,4} |
| static const std::string | file_name =".pro" |
| static const std::string | table_name ="QUARTETS" |
| static const bool | binary =true |
| Static Public Attributes inherited from Data | |
| static const std::string | file_name =".txt" |
| The read function must be defined in the child class. More... | |
| static const std::string | table_name ="NONE" |
| The read function must be defined in the child class. More... | |
Private Member Functions | |
| void | write (std::ostream &out) const |
| The write function must be defined in the child class. | |
| void | read (std::istream &in) |
| The read function must be defined in the child class. | |
Static Private Member Functions | |
| static Data * | create (const std::vector< std::string > &Columns) |
Private Attributes | |
| std::vector< std::string > | sample_names_ |
| names of the samples sequenced. | |
Static Private Attributes | |
| static const Registration | registered =Registration(Locus::table_name, Locus::create) |
Friends | |
| std::istream & | mpileup (std::istream &in, Locus &x, const int &, const int &) |
| void | scan (const Locus &site, const std::string &str, quartet_t &q) |
Additional Inherited Members | |
| Static Public Member Functions inherited from Data | |
| static Data * | new_from_str (const std::string &, const std::vector< std::string > &) |
| Constructs an instance of the class Registered w/ string. | |
| Protected Attributes inherited from Indexed_data | |
| id1_t | abs_pos_ |
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inline |
| const quartet_t & Locus::get_quartet | ( | const count_t & | c | ) | const |
Returns the N'th quartet at the Locus.
returns quartet_t c.
| quartet_t & Locus::get_quartet | ( | const count_t & | c | ) |
Returns the N'th quartet at the Locus.
returns quartet_t c.
| const count_t Locus::getindex | ( | count_t | c | ) | const |
Returns the index of the alleles in order a sorted order.
}
| void Locus::mask | ( | const std::vector< size_t > & | s | ) |
Mask all lines.
Mask all the quartets in the populations in the vector.
| void Locus::maskall | ( | void | ) |
Mask all lines.
Mask all the quartets at this locus.
| void Locus::resize | ( | const size_t & | c | ) |
| void Locus::set_quartet | ( | const quartet_t & | q, |
| const count_t & | c | ||
| ) |
Sets the quartet_t array (unsorted).
sets quartet_t c to q.
| void Locus::unmask | ( | const std::vector< size_t > & | s | ) |
Unmask all lines.
Unmask all the quartets in the populations in the vector.
| void Locus::unmaskall | ( | void | ) |
Unmask all lines.
Unmask all the quartets at this locus.
1.8.6
