glfHandler Class Reference

Collaboration diagram for glfHandler:

Public Member Functions
bool	Open (const String &filename)
void	OpenStub ()
bool	Create (const String &filename)
bool	isOpen ()
void	Close ()
void	Rewind ()
bool	NextSection ()
bool	NextEntry ()
bool	NextBaseEntry ()
void	BeginSection (const String &sectionLabel, int sectionLength)
void	EndSection ()
void	WriteEntry (int outputPosition)
char	GetReference (int position, char defaultBase)
int	GetDepth (int position)
const double *	GetLikelihoods (int position)
const unsigned char *	GetLogLikelihoods (int position)
int	GetMapQuality (int position)

Static Public Member Functions
static const double *	GetDefaultLikelihoods ()
static const unsigned char *	GetDefaultLogLikelihoods ()
static int	GenotypeIndex (int base1, int base2)

Public Attributes
bool	isStub
IFILE	handle
String	header
String	label
int	sections
int	currentSection
int	maxPosition
bool	endOfSection
glfEntry	data
int	position
double	likelihoods [10]
String	indelSequence [2]
const char *	errorMsg

Detailed Description

Definition at line 72 of file glfHandler.h.

Constructor & Destructor Documentation

glfHandler()

glfHandler::glfHandler

(

)

Definition at line 26 of file glfHandler.cpp.

{
    isStub = true;
    sections = 0;
    currentSection = 0;
    maxPosition = position = endOfSection = 0;
}

~glfHandler()

glfHandler::~glfHandler

(

)

Definition at line 34 of file glfHandler.cpp.

{
    // Not safe to close the file here in case a copy of the file was generated
    // if (isOpen())
    //   Close();
}

Member Function Documentation

BeginSection()

void glfHandler::BeginSection	(	const String &	sectionLabel,
		int	sectionLength )

Definition at line 355 of file glfHandler.cpp.

{
    int labelLength = sectionLabel.Length() + 1;
 
    ifwrite(handle, &labelLength, sizeof(int));
    ifwrite(handle, (void *)(const char *) sectionLabel, labelLength);
    ifwrite(handle, &sectionLength, sizeof(int));
 
    label = sectionLabel;
    maxPosition = sectionLength;
}

Close()

void glfHandler::Close

(

)

Definition at line 147 of file glfHandler.cpp.

{
    if (isOpen())
        ifclose(handle);
}

Create()

bool glfHandler::Create

(

const String &

filename

)

Definition at line 71 of file glfHandler.cpp.

{
    isStub = false;
    // glf is in BGZF format.
    handle = ifopen(filename, "wb", InputFile::BGZF);
 
    if (handle == NULL)
    {
        isStub = true;
        return false;
    }
 
    WriteHeader();
 
    return handle != NULL;
}

EndSection()

void glfHandler::EndSection

(

)

Definition at line 367 of file glfHandler.cpp.

{
    char marker = 0;
 
    ifwrite(handle, &marker, sizeof(char));
}

GenotypeIndex()

int glfHandler::GenotypeIndex ( int base1, int base2 )

inlinestatic

Definition at line 132 of file glfHandler.h.

    {
        return base1 < base2 ? (base1 - 1) *(10 - base1) / 2 + (base2 - base1) :
               (base2 - 1) *(10 - base2) / 2 + (base1 - base2);
    }

GetDefaultLikelihoods()

const double * glfHandler::GetDefaultLikelihoods ( )

inlinestatic

Definition at line 123 of file glfHandler.h.

    {
        return nullLikelihoods;
    }

GetDefaultLogLikelihoods()

const unsigned char * glfHandler::GetDefaultLogLikelihoods ( )

inlinestatic

Definition at line 127 of file glfHandler.h.

    {
        return nullLogLikelihoods;
    }

GetDepth()

int glfHandler::GetDepth

(

int

position

)

Definition at line 327 of file glfHandler.cpp.

{
    if (pos == position)
        return data.depth;
 
    return 0;
}

GetLikelihoods()

const double * glfHandler::GetLikelihoods

(

int

position

)

Definition at line 303 of file glfHandler.cpp.

{
    if (pos == position)
        return likelihoods;
 
    return nullLikelihoods;
}

GetLogLikelihoods()

const unsigned char * glfHandler::GetLogLikelihoods

(

int

position

)

Definition at line 311 of file glfHandler.cpp.

{
    if (pos == position)
        return data.lk;
 
    return nullLogLikelihoods;
}

GetMapQuality()

int glfHandler::GetMapQuality

(

int

position

)

Definition at line 335 of file glfHandler.cpp.

{
    if (pos == position)
        return data.mapQuality;
 
    return 0;
}

GetReference()

char glfHandler::GetReference	(	int	position,
		char	defaultBase )

Definition at line 319 of file glfHandler.cpp.

{
    if (pos == position)
        return data.refBase;
 
    return defaultBase;
}

isOpen()

bool glfHandler::isOpen

(

)

Definition at line 88 of file glfHandler.cpp.

{
    return handle != NULL;
}

NextBaseEntry()

bool glfHandler::NextBaseEntry

(

)

Definition at line 200 of file glfHandler.cpp.

{
    bool result = true;
 
    do
    {
        result = NextEntry();
    }
    while (result && data.recordType == 2);
 
    return result;
}

NextEntry()

bool glfHandler::NextEntry

(

)

Definition at line 214 of file glfHandler.cpp.

{
    if (isStub)
        return false;
 
    // Read record type
    if (endOfSection || (ifread(handle, &data, 1) != 1))
    {
        endOfSection = true;
        data.recordType = 0;
        position = maxPosition + 1;
        return false;
    }
 
    // printf("%d/%d\n", data.recordType, data.refBase);
 
    if (position > maxPosition)
        return true;
 
    switch (data.recordType)
    {
        case 0 :
            endOfSection = true;
            position = maxPosition + 1;
            return true;
        case 1 :
            if (ifread(handle,((char *) &data) + 1, sizeof(data) - 1) == sizeof(data) - 1)
            {
                data.refBase = translateBase[data.refBase];
 
                for (int i = 0; i < 10; i++)
                    likelihoods[i] = bQualityConvertor.toDouble(data.lk[i]);
 
                position = position + data.offset;
                return true;
            }
 
            // Premature end of file
            data.recordType = 0;
            position = maxPosition + 1;
            return false;
        case 2 :
            while (ifread(handle, ((char *) &data) + 1, sizeof(data) - 4) == sizeof(data) - 4)
            {
                data.refBase = translateBase[data.refBase];
 
                for (int i = 0; i < 3; i++)
                    likelihoods[i] = bQualityConvertor.toDouble(data.indel.lk[i]);
 
                position = position + data.offset;
 
                indelSequence[0].SetLength(abs(data.indel.length[0]) + 1);
                indelSequence[0][abs(data.indel.length[0])] = 0;
                if (ifread(handle, indelSequence[0].LockBuffer(), abs(data.indel.length[0])) != (unsigned int) abs(data.indel.length[0]))
                    break;
 
                indelSequence[1].SetLength(abs(data.indel.length[1]) + 1);
                indelSequence[1][abs(data.indel.length[1])] = 0;
                if (ifread(handle, indelSequence[1].LockBuffer(), abs(data.indel.length[1])) != (unsigned int) abs(data.indel.length[1]))
                    break;
 
                return true;
            }
 
            // Premature end of file
            data.recordType = 0;
            position = maxPosition + 1;
            return false;
    }
 
    return false;
}

NextSection()

bool glfHandler::NextSection

(

)

Definition at line 166 of file glfHandler.cpp.

{
    if (isStub)
    {
        endOfSection = true;
        data.recordType = 0;
        maxPosition = 1999999999;
        position = maxPosition + 1;
        return true;
    }
 
    while (!endOfSection && !ifeof(handle))
        NextEntry();
 
    endOfSection = false;
 
    int labelLength = 0;
 
    currentSection++;
    position = 0;
    if (ifread(handle, &labelLength, sizeof(int)) == sizeof(int))
    {
        ifread(handle, label.LockBuffer(labelLength+1), labelLength * sizeof(char));
        label.UnlockBuffer();
 
        maxPosition = 0;
        ifread(handle, &maxPosition, sizeof(int));
 
        return ((maxPosition > 0) && !ifeof(handle));
    }
 
    return false;
}

Open()

bool glfHandler::Open

(

const String &

filename

)

Definition at line 41 of file glfHandler.cpp.

{
    isStub = false;
    handle = ifopen(filename, "rb");
 
    if (handle == NULL)
    {
        isStub = true;
        return false;
    }
 
    if (!ReadHeader())
        ifclose(handle);
 
    endOfSection = true;
 
    return handle != NULL;
}

OpenStub()

void glfHandler::OpenStub

(

)

Definition at line 60 of file glfHandler.cpp.

{
    isStub = true;
    handle = NULL;
 
    endOfSection = true;
    data.recordType = 0;
    maxPosition = 1999999999;
    position = maxPosition + 1;
}

Rewind()

void glfHandler::Rewind

(

)

Definition at line 153 of file glfHandler.cpp.

{
    if (isOpen())
    {
        ifrewind(handle);
 
        if (!ReadHeader())
            ifclose(handle);
 
        endOfSection = true;
    }
}

WriteEntry()

void glfHandler::WriteEntry

(

int

outputPosition

)

Definition at line 374 of file glfHandler.cpp.

{
    data.offset = outputPosition - position;
    position = outputPosition;
 
    switch (data.recordType)
    {
        case 0 :
            EndSection();
            return;
        case 1 :
            data.refBase = backTranslateBase[data.refBase];
            ifwrite(handle, &data, sizeof(data));
            data.refBase = translateBase[data.refBase];
            return;
        case 2 :
            data.refBase = backTranslateBase[data.refBase];
            ifwrite(handle, &data, sizeof(data) - 3);
            data.refBase = translateBase[data.refBase];
 
            ifwrite(handle, (void *)(const char *) indelSequence[0], abs(data.indel.length[0]));
            ifwrite(handle, (void *)(const char *) indelSequence[1], abs(data.indel.length[1]));
            return;
    }
}

Member Data Documentation

currentSection

int glfHandler::currentSection

Definition at line 83 of file glfHandler.h.

data

glfEntry glfHandler::data

Definition at line 90 of file glfHandler.h.

endOfSection

bool glfHandler::endOfSection

Definition at line 87 of file glfHandler.h.

errorMsg

const char* glfHandler::errorMsg

Definition at line 96 of file glfHandler.h.

handle

IFILE glfHandler::handle

Definition at line 77 of file glfHandler.h.

header

String glfHandler::header

Definition at line 78 of file glfHandler.h.

indelSequence

String glfHandler::indelSequence[2]

Definition at line 93 of file glfHandler.h.

isStub

bool glfHandler::isStub

Definition at line 76 of file glfHandler.h.

label

String glfHandler::label

Definition at line 81 of file glfHandler.h.

likelihoods

double glfHandler::likelihoods[10]

Definition at line 92 of file glfHandler.h.

maxPosition

int glfHandler::maxPosition

Definition at line 84 of file glfHandler.h.

position

int glfHandler::position

Definition at line 91 of file glfHandler.h.

sections

int glfHandler::sections

Definition at line 82 of file glfHandler.h.

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

• general/glfHandler.h
• general/glfHandler.cpp