PedigreeGlobals Class Reference

Inheritance diagram for PedigreeGlobals:

Collaboration diagram for PedigreeGlobals:

Static Public Member Functions
static int	GetTraitID (const char *name)
static int	GetMarkerID (const char *name)
static int	GetCovariateID (const char *name)
static int	GetAffectionID (const char *name)
static int	GetStringID (const char *name)
static int	LookupTrait (const char *name)
static int	LookupMarker (const char *name)
static int	LookupCovariate (const char *name)
static int	LookupAffection (const char *name)
static int	LookupString (const char *name)
static void	GrowMarkerInfo ()
static MarkerInfo *	GetMarkerInfo (String &name)
static MarkerInfo *	GetMarkerInfo (int marker)
static int	SortMarkersInMapOrder (IntArray &markers, int chromosome=-1)
static void	GetOrderedMarkers (IntArray &markers)
static void	FlagMissingMarkers (IntArray &missingMarkers)
static bool	MarkerPositionsAvailable ()
static bool	AlleleFrequenciesAvailable ()
static void	VerifySexSpecificOrder ()
static void	LoadAlleleFrequencies (const char *filename, bool required=false)
static void	LoadAlleleFrequencies (IFILE &file)
static void	LoadMarkerMap (const char *filename, bool filter=false)
static void	LoadMarkerMap (IFILE &file, bool filter=false)
static void	LoadBasepairMap (const char *filename)
static void	LoadBasepairMap (IFILE &file)
static void	WriteMapFile (const char *filename)
static void	WriteMapFile (FILE *file)
static void	WriteFreqFile (const char *filename, bool old_format=false)
static void	WriteFreqFile (FILE *file, bool old_format=false)
static int	LoadAllele (int marker, String &label)
static int	LoadAllele (MarkerInfo *info, String &label)

Static Public Attributes
static int	traitCount = 0
static int	markerCount = 0
static int	affectionCount = 0
static int	covariateCount = 0
static int	stringCount = 0
static bool	chromosomeX = false
static bool	sexSpecificMap = false
static StringArray	traitNames
static StringArray	covariateNames
static StringArray	affectionNames
static StringArray	markerNames
static StringArray	stringNames
static StringIntHash	markerLookup
static StringIntHash	traitLookup
static StringIntHash	affectionLookup
static StringIntHash	covariateLookup
static StringIntHash	stringLookup
static int	markerInfoCount = 0
static int	markerInfoSize = 0
static MarkerInfo **	markerInfo = NULL
static StringHash	markerInfoByName
static MarkerInfo **	markerInfoByInteger = NULL

Detailed Description

Definition at line 107 of file PedigreeGlobals.h.

Constructor & Destructor Documentation

PedigreeGlobals()

PedigreeGlobals::PedigreeGlobals ( )

inline

Definition at line 204 of file PedigreeGlobals.h.

    {
        instanceCount++;
    }

~PedigreeGlobals()

PedigreeGlobals::~PedigreeGlobals

(

)

Definition at line 711 of file PedigreeGlobals.cpp.

{
    if (--instanceCount == 0 && markerInfoSize)
    {
        for (int i = 0; i < markerInfoCount; i++)
            delete markerInfo[i];
        delete [] markerInfo;
        delete [] markerInfoByInteger;
    }
}

Member Function Documentation

AlleleFrequenciesAvailable()

bool PedigreeGlobals::AlleleFrequenciesAvailable ( )

static

Definition at line 806 of file PedigreeGlobals.cpp.

{
    for (int i = 0; i < markerInfoCount; i++)
        if (markerInfo[i]->freq.Length() > 1)
            return true;
 
    return false;
}

FlagMissingMarkers()

void PedigreeGlobals::FlagMissingMarkers ( IntArray &  missingMarkers )

static

Definition at line 263 of file PedigreeGlobals.cpp.

{
    int skipped_markers = 0;
 
    if (missingMarkers.Length())
    {
        StringArray names;
 
        printf("These markers couldn't be placed and won't be analysed:");
 
        for (int i = 0; i < missingMarkers.Length(); i++)
            names.Push(GetMarkerInfo(missingMarkers[i])->name);
        names.Sort();
 
        for (int i = 0, line = 80, lines = 0; i < missingMarkers.Length(); i++)
        {
            if (line + names[i].Length() + 1 > 79)
                printf("\n   "), line = 3, lines++;
 
            if (lines < 5)
            {
                printf("%s ", (const char *) names[i]);
                line += names[i].Length() + 1;
            }
            else
                skipped_markers++;
        }
 
        if (skipped_markers)
            printf("as well as %d other unlisted markers...", skipped_markers);
 
        printf("\n\n");
    }
}

GetAffectionID()

int PedigreeGlobals::GetAffectionID ( const char *  name )

static

Definition at line 148 of file PedigreeGlobals.cpp.

{
    int idx = affectionLookup.Integer(name);
 
    if (idx != -1) return idx;
 
    affectionNames.Add(name);
    affectionLookup.SetInteger(name, affectionCount);
    return affectionCount++;
}

GetCovariateID()

int PedigreeGlobals::GetCovariateID ( const char *  name )

static

Definition at line 159 of file PedigreeGlobals.cpp.

{
    int idx = covariateLookup.Integer(name);
 
    if (idx != -1) return idx;
 
    covariateNames.Add(name);
    covariateLookup.SetInteger(name, covariateCount);
    return covariateCount++;
}

GetMarkerID()

int PedigreeGlobals::GetMarkerID ( const char *  name )

static

Definition at line 181 of file PedigreeGlobals.cpp.

{
    int idx = markerLookup.Integer(name);
 
    if (idx != -1) return idx;
 
    markerNames.Add(name);
    markerLookup.SetInteger(name, markerCount);
 
    // Grow the marker info key ...
    if (markerCount == 0)
    {
        markerInfoByInteger = new MarkerInfo * [16];
 
        for (int i = 0; i < 16; i++)
            markerInfoByInteger[i] = NULL;
    }
    else if ((markerCount & (markerCount - 1)) == 0 && markerCount > 15)
    {
        MarkerInfo ** newKey = new MarkerInfo * [markerCount * 2];
 
        for (int i = 0; i < markerCount; i++)
            newKey[i] = markerInfoByInteger[i];
 
        for (int i = markerCount; i < markerCount * 2; i++)
            newKey[i] = NULL;
 
        delete [] markerInfoByInteger;
 
        markerInfoByInteger = newKey;
    }
 
    return markerCount++;
}

GetMarkerInfo() [1/2]

MarkerInfo * PedigreeGlobals::GetMarkerInfo ( int  marker )

static

Definition at line 236 of file PedigreeGlobals.cpp.

{
    if (markerId >= markerCount)
        error("Attempted to retrieve MarkerInfo using out-of-bounds index\n");
 
    if (markerInfoByInteger[markerId] != NULL)
        return markerInfoByInteger[markerId];
    else
        return GetMarkerInfo(markerNames[markerId]);
}

GetMarkerInfo() [2/2]

MarkerInfo * PedigreeGlobals::GetMarkerInfo ( String &  name )

static

Definition at line 216 of file PedigreeGlobals.cpp.

{
    MarkerInfo * info = (MarkerInfo *) markerInfoByName.Object(name);
 
    if (info != NULL) return info;
 
    info = new MarkerInfo(name);
    markerInfoByName.Add(name, info);
 
    if (markerInfoCount >= markerInfoSize)
        GrowMarkerInfo();
 
    markerInfo[markerInfoCount++] = info;
 
    int markerId = LookupMarker(name);
    if (markerId >= 0) markerInfoByInteger[markerId] = info;
 
    return info;
}

GetOrderedMarkers()

void PedigreeGlobals::GetOrderedMarkers ( IntArray &  markers )

static

Definition at line 298 of file PedigreeGlobals.cpp.

{
    if (markers.Length() == 0)
    {
        markers.Dimension(markerCount);
        markers.SetSequence(0, 1);
    }
 
    MarkerInfo ** subset = new MarkerInfo * [markers.Length()];
 
    int count = 0;
    IntArray missingMarkers;
 
    for (int i = 0; i < markers.Length(); i++)
    {
        MarkerInfo * info = GetMarkerInfo(markers[i]);
 
        if (info->chromosome != -1)
            subset[count++] = info;
        else
            missingMarkers.Push(i);
    }
 
    FlagMissingMarkers(missingMarkers);
 
    QuickSort(subset, count, sizeof(MarkerInfo *),
              COMPAREFUNC MarkerInfo::ComparePosition);
 
    markers.Clear();
    for (int i = 0; i < count; i++)
        markers.Push(GetMarkerID(subset[i]->name));
}

GetStringID()

int PedigreeGlobals::GetStringID ( const char *  name )

static

Definition at line 170 of file PedigreeGlobals.cpp.

{
    int idx = stringLookup.Integer(name);
 
    if (idx != -1) return idx;
 
    stringNames.Add(name);
    stringLookup.SetInteger(name, stringCount);
    return stringCount++;
}

GetTraitID()

int PedigreeGlobals::GetTraitID ( const char *  name )

static

Definition at line 137 of file PedigreeGlobals.cpp.

{
    int idx = traitLookup.Integer(name);
 
    if (idx != -1) return idx;
 
    traitNames.Add(name);
    traitLookup.SetInteger(name, traitCount);
    return traitCount++;
}

GrowMarkerInfo()

void PedigreeGlobals::GrowMarkerInfo ( )

static

Definition at line 247 of file PedigreeGlobals.cpp.

{
    int newSize = markerInfoSize ? 2 * markerInfoSize : 32;
 
    MarkerInfo ** newArray = new MarkerInfo * [newSize];
 
    if (markerInfoSize)
    {
        memcpy(newArray, markerInfo, sizeof(MarkerInfo *) * markerInfoSize);
        delete [] markerInfo;
    }
 
    markerInfo = newArray;
    markerInfoSize = newSize;
}

LoadAllele() [1/2]

int PedigreeGlobals::LoadAllele ( int  marker, String &  label  )

static

Definition at line 815 of file PedigreeGlobals.cpp.

{
    return LoadAllele(GetMarkerInfo(marker), token);
}

LoadAllele() [2/2]

int PedigreeGlobals::LoadAllele ( MarkerInfo *  info, String &  label  )

static

Definition at line 820 of file PedigreeGlobals.cpp.

{
    int allele = info->GetAlleleNumber(token);
 
    if (allele >= 0) return allele;
 
    static unsigned char lookup[128];
    static bool init = false;
 
    if (!init)
    {
        init = true;
 
        for (int i = 0; i < 128; i++)
            lookup[i] = 0;
 
        for (int i = '1'; i <= '9'; i++)
            lookup[i] = 1;
 
        lookup[int('a')] = lookup[int('A')] = lookup[int('c')] = lookup[int('C')] = 2;
        lookup[int('g')] = lookup[int('G')] = lookup[int('t')] = lookup[int('T')] = 2;
    }
 
    int  first = token[0];
    bool goodstart = first > 0 && first < 128;
 
    if (token.Length() == 1 && goodstart && lookup[int(token[0])])
        return info->NewAllele(token);
 
    if (!goodstart || lookup[int(token[0])] != 1)
        return 0;
 
    int integer = token.AsInteger();
    token = integer;
 
    allele = info->GetAlleleNumber(token);
 
    if (allele > 0)
        return allele;
 
    if (integer <= 0) return 0;
 
    if (integer > 1000000)
    {
        static bool warn_user = true;
 
        if (warn_user)
        {
            printf("Some allele numbers for marker %s are > 1000000\n"
                   "All allele numbers >1000000 will be treated as missing\n\n",
                   (const char *) info->name);
            warn_user = false;
        }
 
        return 0;
    }
 
    return info->NewAllele(token);
}

LoadAlleleFrequencies() [1/2]

void PedigreeGlobals::LoadAlleleFrequencies ( const char *  filename, bool  required = false  )

static

Definition at line 433 of file PedigreeGlobals.cpp.

{
    // This function is often called with an empty string, and not
    // all implementations of the C library like that ...
    if (filename[0] == 0)
    {
        if (required)
            error("No name provided for required allele freuquency file\n");
        else
            return;
    }
 
    // If we get here, the filename is not empty and things should
    // work as planned
    IFILE f = ifopen(filename, "rb");
 
    if (f == NULL)
    {
        if (required)
            error("Failed to open required allele frequency file '%s'",
                  (const char *) filename);
        else
            return;
    }
 
    LoadAlleleFrequencies(f);
    ifclose(f);
}

LoadAlleleFrequencies() [2/2]

void PedigreeGlobals::LoadAlleleFrequencies ( IFILE &  file )

static

Definition at line 462 of file PedigreeGlobals.cpp.

{
    int         done = 0;
    String      buffer;
    StringArray tokens;
    MarkerInfo *info = NULL;
 
    bool need_blank_line = false;
    int  allele_size, old_max, next_allele = 0; // Initialization avoids compiler warning
 
    while (!ifeof(input) && !done)
    {
        int   i, j;
 
        buffer.ReadLine(input);
 
        tokens.Clear();
        tokens.AddTokens(buffer, WHITESPACE);
 
        if (tokens.Length() < 1) continue;
 
        switch (toupper(tokens[0][0]))
        {
            case 'M' :
                if (tokens.Length() == 1)
                    error("Unnamed marker in allele frequency file");
                if (info != NULL)
                    need_blank_line |= info->AdjustFrequencies();
                info = GetMarkerInfo(tokens[1]);
                info->freq.Clear();
                info->freq.Push(0.0);
                next_allele = 1;
                break;
            case 'F' :
                if (info != NULL)
                    for (i = 1; i < tokens.Length(); i++)
                    {
                        buffer = next_allele++;
 
                        int allele = LoadAllele(info, buffer);
 
                        if (allele >= info->freq.Length())
                        {
                            old_max = info->freq.Length();
                            info->freq.Dimension(allele + 1);
                            for (j = old_max; j < allele; j++)
                                info->freq[j] = 0.0;
                        }
 
                        info->freq[allele] = tokens[i].AsDouble();
                    }
                break;
            case 'A' :
                if (info == NULL) continue;
 
                if (tokens.Length() != 3)
                    error("Error reading named allele frequencies for locus %s\n"
                          "Lines with named alleles should have the format\n"
                          "   A allele_label allele_frequency\n\n"
                          "But the following line was read:\n%s\n",
                          (const char *) info->name, (const char *) buffer);
 
                allele_size = LoadAllele(info, tokens[1]);
                next_allele = atoi(tokens[1]) + 1;
 
                if (allele_size < 1)
                    error("Error reading named allele frequencies for locus %s\n"
                          "An invalid allele label was encountered\n",
                          (const char *) info->name);
 
                if (allele_size >= info->freq.Length())
                {
                    old_max = info->freq.Length();
                    info->freq.Dimension(allele_size + 1);
                    for (i = old_max; i < allele_size; i++)
                        info->freq[i] = 0.0;
                }
 
                info->freq[allele_size] = tokens[2];
                break;
            case 'E' :
                done = 1;
                break;
            default :
                error("Problem in allele frequency file.\n"
                      "Lines in this file should be of two types:\n"
                      "  -- Marker name lines begin with an M\n"
                      "  -- Frequency lines begin with an F\n\n"
                      "However the following line is different:\n%s\n",
                      (const char *) buffer);
        }
    }
 
    if (info != NULL)
        need_blank_line |= info->AdjustFrequencies();
 
    if (need_blank_line) printf("\n");
}

LoadBasepairMap() [1/2]

void PedigreeGlobals::LoadBasepairMap ( const char *  filename )

static

Definition at line 656 of file PedigreeGlobals.cpp.

{
    IFILE f = ifopen(filename, "rb");
    if (f == NULL)
        error("The map file [%s] could not be opened\n\n"
              "Please check that the filename is correct and that the file is\n"
              "not being used by another program", filename);
    LoadBasepairMap(f);
    ifclose(f);
}

LoadBasepairMap() [2/2]

void PedigreeGlobals::LoadBasepairMap ( IFILE &  file )

static

Definition at line 667 of file PedigreeGlobals.cpp.

{
    String      buffer;
    StringArray tokens;
 
    sexSpecificMap = false;
 
    while (!ifeof(input))
    {
        buffer.ReadLine(input);
 
        tokens.Clear();
        tokens.AddTokens(buffer, WHITESPACE);
 
        if (tokens.Length() < 1) continue;
 
        if (tokens.Length() != 3)
            error("Error reading map file\n"
                  "Each line in this file should include 3 fields:\n"
                  "CHROMOSOME, MARKER_NAME, and POSITION\n"
                  "However the following line has %d fields\n%s\n",
                  tokens.Length(), (const char *) buffer);
 
        bool previous_state = String::caseSensitive;
        String::caseSensitive = false;
 
        if ((tokens[0] == "CHR" || tokens[0] == "CHROMOSOME") &&
                (tokens[1] == "MARKER" || tokens[1] == "MARKER_NAME" || tokens[1] == "MRK") &&
                (tokens[2] == "BASEPAIR" || tokens[2] == "POS" || tokens[2] == "POSITION"))
            continue;
 
        String::caseSensitive = previous_state;
 
        MarkerInfo * info = GetMarkerInfo(tokens[1]);
 
        int chr = (tokens[0][0] == 'x' || tokens[0][0] == 'X') ? 999 : (int) tokens[0];
 
        info->chromosome = chr;
        info->position = (double) tokens[2];
    }
}

LoadMarkerMap() [1/2]

void PedigreeGlobals::LoadMarkerMap ( const char *  filename, bool  filter = false  )

static

Definition at line 561 of file PedigreeGlobals.cpp.

{
    IFILE f = ifopen(filename, "rb");
    if (f == NULL) return;
    LoadMarkerMap(f, filter);
    ifclose(f);
}

LoadMarkerMap() [2/2]

void PedigreeGlobals::LoadMarkerMap ( IFILE &  file, bool  filter = false  )

static

Definition at line 569 of file PedigreeGlobals.cpp.

{
    String      buffer;
    StringArray tokens;
    bool first_pass = true;
 
    while (!ifeof(input))
    {
        buffer.ReadLine(input);
 
        tokens.Clear();
        tokens.AddTokens(buffer, WHITESPACE);
 
        if (tokens.Length() < 1) continue;
 
        if (first_pass)
        {
            sexSpecificMap = (tokens.Length() == 5);
 
            // if (sexSpecificMap)
            //   printf("\n  Found sex-specific map ...\n\n");
 
            first_pass = false;
        }
 
        if (tokens.Length() != 3 && !sexSpecificMap)
            error("Error reading map file\n"
                  "Each line in this file should include 3 fields:\n"
                  "CHROMOSOME, MARKER_NAME, and POSITION\n"
                  "However the following line has %d fields\n%s\n",
                  tokens.Length(), (const char *) buffer);
 
        if (tokens.Length() != 5 && sexSpecificMap)
            error("Error reading map file\n"
                  "Each line in this file should include 5 fields:\n\n"
                  "CHROMOSOME, MARKER_NAME, SEX_AVERAGED_POS, FEMALE_POS AND MALE_POS\n\n"
                  "However the following line has %d fields\n%s\n",
                  tokens.Length(), (const char *) buffer);
 
        bool previous_state = String::caseSensitive;
        String::caseSensitive = false;
 
        if ((tokens[0] == "CHR" || tokens[0] == "CHROMOSOME") &&
                (tokens[1] == "MARKER" || tokens[1] == "MARKER_NAME" || tokens[1] == "MRK") &&
                (tokens[2] == "KOSAMBI" || tokens[2] == "POS" || tokens[2] == "POSITION" ||
                 tokens[2] == "SEX_AVERAGED_POS" || tokens[2] == "CM" || tokens[2] == "HALDANE"))
            continue;
 
        String::caseSensitive = previous_state;
 
        if (filter)
            if (LookupMarker(tokens[1]) < 0)
                continue;
 
        MarkerInfo * info = GetMarkerInfo(tokens[1]);
 
        int chr = (tokens[0][0] == 'x' || tokens[0][0] == 'X') ? 999 : (int) tokens[0];
 
        info->chromosome = chr;
        info->position = (double) tokens[2] * 0.01;
 
        if (sexSpecificMap)
        {
            char * flag;
 
            double female = strtod(tokens[3], &flag);
            if (*flag)
                error("In the map file, the female cM position for marker\n"
                      "%s is %s. This is not a valid number.",
                      (const char *) tokens[1], (const char *) tokens[3]);
 
            double male = strtod(tokens[4], &flag);
            if (*flag)
                error("In the map file, the male cM position for marker\n"
                      "%s is %s. This is not a valid number.",
                      (const char *) tokens[1], (const char *) tokens[4]);
 
            info->positionFemale = (double) female * 0.01;
            info->positionMale = (double) male * 0.01;
        }
        else
            info->positionFemale = info->positionMale = info->position;
    }
 
    if (sexSpecificMap) VerifySexSpecificOrder();
}

LookupAffection()

static int PedigreeGlobals::LookupAffection ( const char *  name )

inlinestatic

Definition at line 158 of file PedigreeGlobals.h.

    {
        return affectionLookup.Integer(name);
    }

LookupCovariate()

static int PedigreeGlobals::LookupCovariate ( const char *  name )

inlinestatic

Definition at line 154 of file PedigreeGlobals.h.

    {
        return covariateLookup.Integer(name);
    }

LookupMarker()

static int PedigreeGlobals::LookupMarker ( const char *  name )

inlinestatic

Definition at line 150 of file PedigreeGlobals.h.

    {
        return markerLookup.Integer(name);
    }

LookupString()

static int PedigreeGlobals::LookupString ( const char *  name )

inlinestatic

Definition at line 162 of file PedigreeGlobals.h.

    {
        return stringLookup.Integer(name);
    }

LookupTrait()

static int PedigreeGlobals::LookupTrait ( const char *  name )

inlinestatic

Definition at line 146 of file PedigreeGlobals.h.

    {
        return traitLookup.Integer(name);
    }

MarkerPositionsAvailable()

bool PedigreeGlobals::MarkerPositionsAvailable ( )

static

Definition at line 797 of file PedigreeGlobals.cpp.

{
    for (int i = 0; i < markerInfoCount; i++)
        if (markerInfo[i]->chromosome != -1)
            return true;
 
    return false;
}

SortMarkersInMapOrder()

int PedigreeGlobals::SortMarkersInMapOrder ( IntArray &  markers, int  chromosome = -1  )

static

Definition at line 331 of file PedigreeGlobals.cpp.

{
    if (markers.Length() == 0)
    {
        markers.Dimension(markerCount);
        markers.SetSequence(0, 1);
    }
 
    MarkerInfo ** subset = new MarkerInfo * [markers.Length()];
 
    int count = 0;
    IntArray missingMarkers;
 
    for (int i = 0; i < markers.Length(); i++)
    {
        MarkerInfo * info = GetMarkerInfo(markers[i]);
 
        if (info->chromosome != -1)
            subset[count++] = info;
        else if (chromosome == -1)
            missingMarkers.Push(i);
    }
 
    if (chromosome == -1)
        FlagMissingMarkers(missingMarkers);
 
    QuickSort(subset, count, sizeof(MarkerInfo *),
              COMPAREFUNC MarkerInfo::ComparePosition);
 
    markers.Clear();
 
    int  current_chromosome = -1, next_chromosome = 0;
 
    for (int i = 0; i < count; i++)
        if (subset[i]->chromosome < chromosome)
            continue;
        else if (current_chromosome == -1 ||
                 subset[i]->chromosome == current_chromosome)
        {
            markers.Push(GetMarkerID(subset[i]->name));
            current_chromosome = subset[i]->chromosome;
        }
        else if (!next_chromosome)
        {
            next_chromosome = subset[i]->chromosome;
            break;
        }
 
    delete [] subset;
 
    return next_chromosome;
}

VerifySexSpecificOrder()

void PedigreeGlobals::VerifySexSpecificOrder ( )

static

Definition at line 384 of file PedigreeGlobals.cpp.

{
    if (markerCount <= 1)
        return;
 
    MarkerInfo ** sortedMarkers = new MarkerInfo * [markerCount];
 
    for (int i = 0; i < markerCount; i++)
        sortedMarkers[i] = GetMarkerInfo(i);
 
    QuickSort(sortedMarkers, markerCount, sizeof(MarkerInfo *),
              COMPAREFUNC MarkerInfo::ComparePosition);
 
    double prev_female = sortedMarkers[0]->positionFemale;
    double prev_male = sortedMarkers[0]->positionMale;
    double curr_female, curr_male;
 
    int    prev_chromosome = sortedMarkers[0]->chromosome;
    int    curr_chromosome;
 
    for (int i = 1; i < markerCount; i++)
    {
        curr_chromosome = sortedMarkers[i]->chromosome;
        curr_female = sortedMarkers[i]->positionFemale;
        curr_male = sortedMarkers[i]->positionMale;
 
        if (curr_chromosome == prev_chromosome &&
                (curr_female < prev_female || curr_male < prev_male))
            error("Sex-specific and sex-averaged maps are inconsistent.\n\n"
                  "In the sex-averaged map, marker %s (%.2f cM) follows marker %s (%.2f cM).\n"
                  "In the %smale map, marker %s (%.2f cM) PRECEDES marker %s (%.2f cM).\n",
                  (const char *) sortedMarkers[i]->name,
                  sortedMarkers[i]->position * 100,
                  (const char *) sortedMarkers[i-1]->name,
                  sortedMarkers[i-1]->position * 100,
                  curr_female < prev_female ? "fe" : "",
                  (const char *) sortedMarkers[i]->name,
                  (curr_female < prev_female ? curr_female : curr_male) * 100,
                  (const char *) sortedMarkers[i-1]->name,
                  (curr_female < prev_female ? prev_female : prev_male) * 100);
 
        prev_chromosome = curr_chromosome;
        prev_female = curr_female;
        prev_male = curr_male;
    }
 
    delete [] sortedMarkers;
}

WriteFreqFile() [1/2]

void PedigreeGlobals::WriteFreqFile ( const char *  filename, bool  old_format = false  )

static

Definition at line 763 of file PedigreeGlobals.cpp.

{
    FILE * output = fopen(filename, "wt");
 
    if (output == NULL)
        error("Creating allele frequency file \"%s\"", filename);
 
    WriteFreqFile(output, old_format);
    fclose(output);
}

WriteFreqFile() [2/2]

void PedigreeGlobals::WriteFreqFile ( FILE *  file, bool  old_format = false  )

static

Definition at line 774 of file PedigreeGlobals.cpp.

{
    for (int i = 0; i < markerInfoCount; i++)
    {
        MarkerInfo * info = markerInfo[i];
 
        if (info->freq.Length() == 0) continue;
 
        fprintf(output, "M %s\n", (const char *) info->name);
 
        if (old_format && info->alleleLabels.Length() == 0)
            for (int j = 1; j < info->freq.Length(); j++)
                fprintf(output, "%s%.5f%s",
                        j % 7 == 1 ? "F " : "", info->freq[j],
                        j == info->freq.Length() - 1 ? "\n" : j % 7 == 0 ? "\n" : " ");
        else
            for (int j = 1; j < info->freq.Length(); j++)
                if (info->freq[j] > 1e-7)
                    fprintf(output, "A %5s %.5f\n",
                            (const char *) info->GetAlleleLabel(j), info->freq[j]);
    }
}

WriteMapFile() [1/2]

void PedigreeGlobals::WriteMapFile ( const char *  filename )

static

Definition at line 722 of file PedigreeGlobals.cpp.

{
    if (!MarkerPositionsAvailable())
        return;
 
    FILE * output = fopen(filename, "wt");
 
    if (output == NULL)
        error("Creating map file \"%s\"", filename);
 
    WriteMapFile(output);
    fclose(output);
}

WriteMapFile() [2/2]

void PedigreeGlobals::WriteMapFile ( FILE *  file )

static

Definition at line 736 of file PedigreeGlobals.cpp.

{
    if (!sexSpecificMap)
        fprintf(output, "CHR  MARKER    POS\n");
    else
        fprintf(output, "CHR  MARKER    POS   POSF   POSM\n");
 
    for (int i = 0; i < markerInfoCount; i++)
    {
        if (markerInfo[i]->chromosome != -1)
        {
            if (!sexSpecificMap)
                fprintf(output, "%3d  %-10s  %g\n",
                        markerInfo[i]->chromosome,
                        (const char *) markerInfo[i]->name,
                        markerInfo[i]->position * 100.0);
            else
                fprintf(output, "%3d %-10s %g  %g  %g\n",
                        markerInfo[i]->chromosome,
                        (const char *) markerInfo[i]->name,
                        markerInfo[i]->position * 100.0,
                        markerInfo[i]->positionFemale * 100.0,
                        markerInfo[i]->positionMale * 100.0);
        }
    }
}

Member Data Documentation

affectionCount

int PedigreeGlobals::affectionCount = 0

static

Definition at line 112 of file PedigreeGlobals.h.

affectionLookup

StringIntHash PedigreeGlobals::affectionLookup

static

Definition at line 129 of file PedigreeGlobals.h.

affectionNames

StringArray PedigreeGlobals::affectionNames

static

Definition at line 124 of file PedigreeGlobals.h.

chromosomeX

bool PedigreeGlobals::chromosomeX = false

static

Definition at line 117 of file PedigreeGlobals.h.

covariateCount

int PedigreeGlobals::covariateCount = 0

static

Definition at line 113 of file PedigreeGlobals.h.

covariateLookup

StringIntHash PedigreeGlobals::covariateLookup

static

Definition at line 130 of file PedigreeGlobals.h.

covariateNames

StringArray PedigreeGlobals::covariateNames

static

Definition at line 123 of file PedigreeGlobals.h.

markerCount

int PedigreeGlobals::markerCount = 0

static

Definition at line 111 of file PedigreeGlobals.h.

markerInfo

MarkerInfo ** PedigreeGlobals::markerInfo = NULL

static

Definition at line 169 of file PedigreeGlobals.h.

markerInfoByInteger

MarkerInfo ** PedigreeGlobals::markerInfoByInteger = NULL

static

Definition at line 171 of file PedigreeGlobals.h.

markerInfoByName

StringHash PedigreeGlobals::markerInfoByName

static

Definition at line 170 of file PedigreeGlobals.h.

markerInfoCount

int PedigreeGlobals::markerInfoCount = 0

static

Definition at line 167 of file PedigreeGlobals.h.

markerInfoSize

int PedigreeGlobals::markerInfoSize = 0

static

Definition at line 168 of file PedigreeGlobals.h.

markerLookup

StringIntHash PedigreeGlobals::markerLookup

static

Definition at line 127 of file PedigreeGlobals.h.

markerNames

StringArray PedigreeGlobals::markerNames

static

Definition at line 125 of file PedigreeGlobals.h.

sexSpecificMap

bool PedigreeGlobals::sexSpecificMap = false

static

Definition at line 120 of file PedigreeGlobals.h.

stringCount

int PedigreeGlobals::stringCount = 0

static

Definition at line 114 of file PedigreeGlobals.h.

stringLookup

StringIntHash PedigreeGlobals::stringLookup

static

Definition at line 131 of file PedigreeGlobals.h.

stringNames

StringArray PedigreeGlobals::stringNames

static

Definition at line 126 of file PedigreeGlobals.h.

traitCount

int PedigreeGlobals::traitCount = 0

static

Definition at line 110 of file PedigreeGlobals.h.

traitLookup

StringIntHash PedigreeGlobals::traitLookup

static

Definition at line 128 of file PedigreeGlobals.h.

traitNames

StringArray PedigreeGlobals::traitNames

static

Definition at line 122 of file PedigreeGlobals.h.

---

The documentation for this class was generated from the following files:

• general/PedigreeGlobals.h
• general/PedigreeGlobals.cpp