25#include "PedigreeAlleles.h"
26#include "PedigreePerson.h"
27#include "PedigreeGlobals.h"
28#include "PedigreeFamily.h"
29#include "PedigreeDescription.h"
30#include "PedigreeAlleleFreq.h"
35 static bool sexAsCovariate;
52 void Prepare(
IFILE & input);
53 void Load(
IFILE & input);
54 void LoadMendel(
IFILE & input);
55 void Prepare(
const char * input);
59 void Load(
const char * input,
bool allowFailures =
false);
62 int TranslateSexCode(
const char * code,
bool & failure);
64 void PrepareDichotomization();
65 int Dichotomize(
int trait,
double mean = _NAN_);
66 void DichotomizeAll(
double mean = _NAN_);
68 void WriteDataFile(FILE * output);
69 void WritePedigreeFile(FILE * output);
70 void WriteDataFile(
const char * output);
71 void WritePedigreeFile(
const char * output);
72 void WritePerson(FILE * output,
int who,
73 const char * famid = NULL,
74 const char * pid = NULL,
75 const char * fatid = NULL,
76 const char * motid = NULL);
77 void WriteRecodedPerson(
78 FILE * output,
int who,
80 const char * famid = NULL,
81 const char * pid = NULL,
82 const char * fatid = NULL,
83 const char * motid = NULL);
86 Family * FindFamily(
const char * famid);
87 Person * FindPerson(
const char * famid,
92 int CountAlleles(
int marker);
96 void LumpAlleles(
double treshold,
bool reorder =
true);
99 void EstimateFrequencies(
int estimator,
bool quiet =
false);
102 Person & operator [](
int i)
104 return *(persons[i]);
108 bool InheritanceCheck(
bool abortIfInconsistent =
true);
109 bool AutosomalCheck();
110 bool SexLinkedCheck();
117 void Trim(
bool quiet =
false,
int * informative = NULL);
120 void AddPerson(
const char * famid,
const char * pid,
121 const char * fatid,
const char * motid,
122 int sex,
bool delay_sort =
false);
125 void ExtractFamily(
int id,
Pedigree & new_ped);
127 void ExtractOnAffection(
int a,
Pedigree & new_ped,
int target_status = 2);
133 void ShowMemoryInfo();
139 static int ComparePersons(
const Person ** p1,
const Person ** p2);
140 static int CompareParents(
const Person ** p1,
const Person ** p2);
145 Person * FindPerson(
const char * famid,
const char * pid,
int universe);
147 void ShowTrimHeader(
bool & flag);