GlfRecord Class Reference

This class allows a user to easily get/set the fields in a GLF record. More...

#include <GlfRecord.h>

List of all members.

Public Member Functions
	GlfRecord ()
	Constructor.
	~GlfRecord ()
	Destructor.
void	reset ()
	Clear this record back to the default setting.
bool	read (IFILE filePtr)
	Read the record from the specified file (file MUST be in the correct position for reading a record).
bool	write (IFILE filePtr) const
	Write the record to the specified file.
void	print () const
	Print the reference section in a readable format.
Generic Accessors for Record Types 1 & 2
bool	setRtypeRef (uint8_t rtypeRef)
	Set the record type and reference base.
bool	setRecordType (uint8_t recType)
	Set the record type.
bool	setRefBaseInt (uint8_t refBase)
	Set the reference base from an integer value.
bool	setOffset (uint32_t offset)
	Set the offset from the precedent record.
bool	setMinDepth (uint32_t minDepth)
	Set the minimum likelihood and the read depth.
bool	setMinLk (uint8_t minLk)
	Set the minimum likelihood.
bool	setReadDepth (uint32_t readDepth)
	Set the the read depth.
bool	setRmsMapQ (uint8_t rmsMapQ)
	Set the RMS of mapping qualities of reads covering the site.
int	getRecordType () const
	Return the record type.
int	getRefBase () const
	Return the reference base as an integer.
char	getRefBaseChar () const
	Return the reference base as a character.
uint32_t	getOffset () const
	Return the offset from the precedent record.
uint32_t	getMinDepth () const
	Return the minimum likelihood and read depth.
uint8_t	getMinLk () const
	Return the minimum likelihood.
uint32_t	getReadDepth () const
	Return the read depth.
uint8_t	getRmsMapQ () const
	Return the RMS of mapping qualities of reads covering the site.
Record Type 1 Accessors
Record Type 1: Simple Likelihood Record
bool	setLk (int index, uint8_t value)
	Set the likelihood for the specified genotype.
uint8_t	getLk (int index)
	Get the likelihood for the specified genotype index.
Record Type 2 Accessors
Record Type2: Indel Likelihood Record
bool	setLkHom1 (uint8_t lk)
	Set the likelihood of the first homozygous indel allele.
bool	setLkHom2 (uint8_t lk)
	Set the likelihood of the 2nd homozygous indel allele.
bool	setLkHet (uint8_t lk)
	Set the likelihood of a heterozygote.
bool	setInsertionIndel1 (const std::string &indelSeq)
	Set the sequence of the first indel allele if the first indel is an insertion.
bool	setDeletionIndel1 (const std::string &indelSeq)
	Set the sequence of the first indel allele if the first indel is an deletion.
bool	setInsertionIndel2 (const std::string &indelSeq)
	Set the sequence of the 2nd indel allele if the 2nd indel is an insertion.
bool	setDeletionIndel2 (const std::string &indelSeq)
	Set the sequence of the 2nd indel allele if the 2nd indel is an deletion.
uint8_t	getLkHom1 ()
	Return the likelihood of the 1st homozygous indel allele.
uint8_t	getLkHom2 ()
	Return the likelihood of the 2nd homozygous indel allele.
uint8_t	getLkHet ()
	Return the likelihood of a heterozygote.
int16_t	getIndel1 (std::string &indelSeq)
	Get the sequence and length (+:ins, -:del) of the 1st indel allele.
int16_t	getIndel2 (std::string &indelSeq)
	Get the sequence and length (+:ins, -:del) of the 2nd indel allele.

---

Detailed Description

This class allows a user to easily get/set the fields in a GLF record.

Definition at line 28 of file GlfRecord.h.

---

Member Function Documentation

int16_t GlfRecord::getIndel1

(

std::string &

indelSeq

)

Get the sequence and length (+:ins, -:del) of the 1st indel allele.

Parameters:

indelSeq

string to set with the sequence of the 1st indel allele

Returns:

length of the 1st indel allele (positive=insertion; negative=deletion; 0=no-indel)

Definition at line 453 of file GlfRecord.cpp.

References getRecordType(), and GlfStatus::UNKNOWN.

{
    if(getRecordType() != 2)
    {
        throw(GlfException(GlfStatus::UNKNOWN, 
                           "Tried to call getIndel1 for Record not of type 2."));
        return(0);
    }
    indelSeq = myIndelSeq1.c_str();
    return(myRec2Base.indelLen1);
}

int16_t GlfRecord::getIndel2

(

std::string &

indelSeq

)

Get the sequence and length (+:ins, -:del) of the 2nd indel allele.

Parameters:

indelSeq

string to set with the sequence of the 2nd indel allele

Returns:

length of the 2nd indel allele (positive=insertion; negative=deletion; 0=no-indel)

Definition at line 465 of file GlfRecord.cpp.

References getRecordType(), and GlfStatus::UNKNOWN.

{
    if(getRecordType() != 2)
    {
        throw(GlfException(GlfStatus::UNKNOWN, 
                           "Tried to call getIndel2 for Record not of type 2."));
        return(0);
    }
    indelSeq = myIndelSeq2.c_str();
    return(myRec2Base.indelLen2);
}

uint8_t GlfRecord::getLk

(

int

index

)

Get the likelihood for the specified genotype index.

Throws an exception if index is out of range.

Parameters:

index

index of the genotype for which the likelihood should be returned. See: GenotypeIndexTable

Returns:

likelihood of the specified index.

Definition at line 355 of file GlfRecord.cpp.

References getRecordType(), and GlfStatus::UNKNOWN.

{
    if(getRecordType() != 1)
    {
        throw(GlfException(GlfStatus::UNKNOWN, 
                           "Tried to call getLk for Record not of type 1."));
        return(0);
    }
    if((index < 0) || (index >= NUM_REC1_LIKELIHOOD))
    {
        throw(GlfException(GlfStatus::UNKNOWN, 
                           "Tried to call getLk for index < 0 or >= 10."));
        return(0);
    }
    return(myRec1Base.lk[index]);
}

uint8_t GlfRecord::getLkHet

(

)

Return the likelihood of a heterozygote.

Returns:

likelihood of a hetereozygote.

Definition at line 442 of file GlfRecord.cpp.

References getRecordType(), and GlfStatus::UNKNOWN.

{
    if(getRecordType() != 2)
    {
        throw(GlfException(GlfStatus::UNKNOWN, 
                           "Tried to call getLkHet for Record not of type 2."));
        return(0);
    }
    return(myRec2Base.lkHet);
}

uint8_t GlfRecord::getLkHom1

(

)

Return the likelihood of the 1st homozygous indel allele.

Returns:

likelihood of the 1st homozygous indel allele.

Definition at line 420 of file GlfRecord.cpp.

References getRecordType(), and GlfStatus::UNKNOWN.

{
    if(getRecordType() != 2)
    {
        throw(GlfException(GlfStatus::UNKNOWN, 
                           "Tried to call getLkHom1 for Record not of type 2."));
        return(0);
    }
    return(myRec2Base.lkHom1);
}

uint8_t GlfRecord::getLkHom2

(

)

Return the likelihood of the 2nd homozygous indel allele.

Returns:

likelihood of the 2nd homozygous indel allele.

Definition at line 431 of file GlfRecord.cpp.

References getRecordType(), and GlfStatus::UNKNOWN.

{
    if(getRecordType() != 2)
    {
        throw(GlfException(GlfStatus::UNKNOWN, 
                           "Tried to call getLkHom2 for Record not of type 2."));
        return(0);
    }
    return(myRec2Base.lkHom2);
}

uint32_t GlfRecord::getMinDepth

(

)

const

Return the minimum likelihood and read depth.

Formatted as: min_lk<<24|read_dpeth. (min_lk capped at 255)

Returns:

minimum likelihood and read depth

Definition at line 278 of file GlfRecord.cpp.

References getRecordType(), and GlfStatus::UNKNOWN.

{
    if(getRecordType() == 1)
    {
        return(myRec1Base.min_depth);
    }
    else if(getRecordType() == 2)
    {
        return(myRec2Base.min_depth);
    }
    throw(GlfException(GlfStatus::UNKNOWN, 
                       "Tried to call getMinDepth for Record not of type 1 or 2."));
    return(0);
}

uint8_t GlfRecord::getMinLk

(

)

const

Return the minimum likelihood.

Returns:

minimum likelihood

Definition at line 293 of file GlfRecord.cpp.

References getRecordType(), and GlfStatus::UNKNOWN.

{
    if(getRecordType() == 1)
    {
        return(myRec1Base.min_depth >> MIN_LK_SHIFT);
    }
    else if(getRecordType() == 2)
    {
        return(myRec2Base.min_depth >> MIN_LK_SHIFT);
    }
    throw(GlfException(GlfStatus::UNKNOWN, 
                       "Tried to call getMinLk for Record not of type 1 or 2."));
    return(0);
}

uint32_t GlfRecord::getOffset

(

)

const

Return the offset from the precedent record.

Returns:

offset from the precedent record.

Definition at line 263 of file GlfRecord.cpp.

References getRecordType(), and GlfStatus::UNKNOWN.

{
    if(getRecordType() == 1)
    {
        return(myRec1Base.offset);
    }
    else if(getRecordType() == 2)
    {
        return(myRec2Base.offset);
    }
    throw(GlfException(GlfStatus::UNKNOWN, 
                       "Tried to call getOffset for Record not of type 1 or 2."));
    return(0);
}

uint32_t GlfRecord::getReadDepth

(

)

const

Return the read depth.

Returns:

read depth

Definition at line 308 of file GlfRecord.cpp.

References getRecordType(), and GlfStatus::UNKNOWN.

{
    if(getRecordType() == 1)
    {
        return(myRec1Base.min_depth & READ_DEPTH_MASK);
    }
    else if(getRecordType() == 2)
    {
        return(myRec2Base.min_depth & READ_DEPTH_MASK);
    }
    throw(GlfException(GlfStatus::UNKNOWN, 
                       "Tried to call getReadDepth for Record not of type 1 or 2."));
    return(0);
}

int GlfRecord::getRecordType

(

)

const [inline]

Return the record type.

Returns:

record type for this record: 0 - endMarker, 1 - simple likelihood, 2 - indel likelihood

Definition at line 126 of file GlfRecord.h.

Referenced by getIndel1(), getIndel2(), getLk(), getLkHet(), getLkHom1(), getLkHom2(), getMinDepth(), getMinLk(), GlfFile::getNextRecord(), getOffset(), getReadDepth(), getRmsMapQ(), print(), read(), write(), and GlfFile::writeRecord().

    {
        return(myRecTypeRefBase >> REC_TYPE_SHIFT);
    }

int GlfRecord::getRefBase

(

)

const [inline]

Return the reference base as an integer.

Returns:

integer representation of the reference base. See: BaseCharacterIntMap

Definition at line 134 of file GlfRecord.h.

Referenced by print().

    {
        return(myRecTypeRefBase & REF_BASE_MASK);
    }

char GlfRecord::getRefBaseChar

(

)

const

Return the reference base as a character.

Returns:

character representation of the reference base.

Definition at line 251 of file GlfRecord.cpp.

Referenced by print().

{
    int index = myRecTypeRefBase & REF_BASE_MASK;
    if((index > REF_BASE_MAX) || (index < 0))
    {
        // TODO throw exception.
        return('N');
    }
    return(REF_BASE_CHAR[index]);
}

uint8_t GlfRecord::getRmsMapQ

(

)

const

Return the RMS of mapping qualities of reads covering the site.

Returns:

RMS of maping qualities.

Definition at line 323 of file GlfRecord.cpp.

References getRecordType(), and GlfStatus::UNKNOWN.

{
    if(getRecordType() == 1)
    {
        return(myRec1Base.rmsMapQ);
    }
    else if(getRecordType() == 2)
    {
        return(myRec2Base.rmsMapQ);
    }
    throw(GlfException(GlfStatus::UNKNOWN, 
                       "Tried to call getRmsMapQ for Record not of type 1 or 2."));
    return(0);
}

bool GlfRecord::read

(

IFILE

filePtr

)

Read the record from the specified file (file MUST be in the correct position for reading a record).

Parameters:

filePtr

file to read from that is in the correct position.

Returns:

true if the record was successfully read from the file (even if it is an endMarker), false if it was not successfully read.

Definition at line 65 of file GlfRecord.cpp.

References GlfStatus::FAIL_IO, getRecordType(), ifread(), and GlfStatus::INVALID.

Referenced by GlfFile::getNextRecord().

{
    // Read the record type and reference base.
    int numRead = 0;
    int byteLen = sizeof(uint8_t);
    numRead = ifread(filePtr, &myRecTypeRefBase, byteLen);
    if(numRead != byteLen)
    {
        String errorMsg = "Failed to read the record type & reference base (";
        errorMsg += byteLen;
        errorMsg += " bytes).  Only read ";
        errorMsg += numRead;
        errorMsg += " bytes.";
        std::string errorString = errorMsg.c_str();
        throw(GlfException(GlfStatus::FAIL_IO, errorString));
        return(false);
    }

    // TODO, split up by types of records...
    switch(getRecordType())
    {
        case 0:
            //  Last record.
            // Nothing more to read.
            break;
        case 1:
            // Read type 1.
            readType1(filePtr);
            break;
        case 2:
            // Read type 2.
            readType2(filePtr);
            break;
        default:
            String errorMsg = "Failed to read the record: unknown type: ";
            errorMsg += getRecordType();
            std::string errorString = errorMsg.c_str();
            throw(GlfException(GlfStatus::INVALID, errorString));
            return(false);
            break;
    };

    // Successfully read, return success.
    return(true);
}

bool GlfRecord::setDeletionIndel1

(

const std::string &

indelSeq

)

Set the sequence of the first indel allele if the first indel is an deletion.

Parameters:

indelSeq

sequence of the first indel allele (deletion).

Returns:

true if successfully set, false if not.

Definition at line 399 of file GlfRecord.cpp.

{
    myRec2Base.indelLen1 = 0 - (indelSeq.length());
    myIndelSeq1 = indelSeq;
    return(true);
}

bool GlfRecord::setDeletionIndel2

(

const std::string &

indelSeq

)

Set the sequence of the 2nd indel allele if the 2nd indel is an deletion.

Parameters:

indelSeq

sequence of the 2nd indel allele (deletion).

Returns:

true if successfully set, false if not.

Definition at line 413 of file GlfRecord.cpp.

{
    myRec2Base.indelLen2 = 0 - (indelSeq.length());
    myIndelSeq2 = indelSeq;
    return(true);
}

bool GlfRecord::setInsertionIndel1

(

const std::string &

indelSeq

)

Set the sequence of the first indel allele if the first indel is an insertion.

Parameters:

indelSeq

sequence of the first indel allele (insertion).

Returns:

true if successfully set, false if not.

Definition at line 392 of file GlfRecord.cpp.

{
    myRec2Base.indelLen1 = indelSeq.length();
    myIndelSeq1 = indelSeq;
    return(true);
}

bool GlfRecord::setInsertionIndel2

(

const std::string &

indelSeq

)

Set the sequence of the 2nd indel allele if the 2nd indel is an insertion.

Parameters:

indelSeq

sequence of the 2nd indel allele (insertion).

Returns:

true if successfully set, false if not.

Definition at line 406 of file GlfRecord.cpp.

{
    myRec2Base.indelLen2 = indelSeq.length();
    myIndelSeq2 = indelSeq;
    return(true);
}

bool GlfRecord::setLk	(	int	index,
		uint8_t	value
	)

Set the likelihood for the specified genotype.

Throws an exception if index is out of range.

Parameters:

index	index for the genotype for which the likelihood is being set. Index 0 1 2 3 4 5 6 7 8 9 Genotype AA AC AG AT CC CG CT GG GT TT
value	likelihood for the genotype at the specified index.

Returns:

true if successfully set, false if not.

Definition at line 340 of file GlfRecord.cpp.

References GlfStatus::UNKNOWN.

{
    if((index < 0) || (index >= NUM_REC1_LIKELIHOOD))
    {
        //  Out of range.
        throw(GlfException(GlfStatus::UNKNOWN, 
                           "Trying to set Record Type 1 likelihood position< 0 or >= 10."));
        return(false);
    }

    // In range.
    myRec1Base.lk[index] = value;
    return(true);
}

bool GlfRecord::setLkHet

(

uint8_t

lk

)

Set the likelihood of a heterozygote.

Parameters:

lk	likelihood of a heterozygote (capped at 255)

Returns:

true if successfully set, false if not.

Definition at line 386 of file GlfRecord.cpp.

{
    myRec2Base.lkHet = lk;
    return(true);
}

bool GlfRecord::setLkHom1

(

uint8_t

lk

)

Set the likelihood of the first homozygous indel allele.

Parameters:

lk	likelihood of the 1st homozygous indel allele (capped at 255)

Returns:

true if successfully set, false if not.

Definition at line 374 of file GlfRecord.cpp.

{
    myRec2Base.lkHom1 = lk;
    return(true);
}

bool GlfRecord::setLkHom2

(

uint8_t

lk

)

Set the likelihood of the 2nd homozygous indel allele.

Parameters:

lk	likelihood of the 2nd homozygous indel allele (capped at 255)

Returns:

true if successfully set, false if not.

Definition at line 380 of file GlfRecord.cpp.

{
    myRec2Base.lkHom2 = lk;
    return(true);
}

bool GlfRecord::setMinDepth

(

uint32_t

minDepth

)

Set the minimum likelihood and the read depth.

Parameters:

minDepth

minimum likelihood and read depth. Formatted as: min_lk<<24|read_dpeth. (min_lk capped at 255)

Returns:

true if successfully set, false if not.

Definition at line 222 of file GlfRecord.cpp.

Referenced by setMinLk(), and setReadDepth().

{
    myRec1Base.min_depth = minDepth;
    myRec2Base.min_depth = minDepth;
    return(true);
}

bool GlfRecord::setMinLk

(

uint8_t

minLk

)

Set the minimum likelihood.

Parameters:

minLk

minimum likelihood (capped at 255).

Returns:

true if successfully set, false if not.

Definition at line 229 of file GlfRecord.cpp.

References setMinDepth().

{
    setMinDepth((myRec1Base.min_depth & READ_DEPTH_MASK) |
                (minLk << MIN_LK_SHIFT));
    return(true);
}

bool GlfRecord::setOffset

(

uint32_t

offset

)

Set the offset from the precedent record.

0-based coordinate of the record minus the coordinate of the precedent record. For the first record in a reference sequence, the previous coordinate is 0. For insertions between x & x+1, the coordinate is x. For deletions between x & y, the coordinate is x.

Parameters:

offset

offset from the precedent record.

Returns:

true if successfully set, false if not.

Definition at line 215 of file GlfRecord.cpp.

{
    myRec1Base.offset = offset;
    myRec2Base.offset = offset;
    return(true);
}

bool GlfRecord::setReadDepth

(

uint32_t

readDepth

)

Set the the read depth.

Parameters:

readDepth

read depth.

Returns:

true if successfully set, false if not.

Definition at line 236 of file GlfRecord.cpp.

References setMinDepth().

{
    setMinDepth((myRec1Base.min_depth & MIN_LK_MASK) |
                (readDepth & READ_DEPTH_MASK));
    return(true);
}

bool GlfRecord::setRecordType

(

uint8_t

recType

)

Set the record type.

Parameters:

recType

record type: 1 - simple likelihood record, 2 - indel likelihood record, 0 - end maker

Returns:

true if the record type was successfully set, false if not.

Definition at line 194 of file GlfRecord.cpp.

{
    myRecTypeRefBase = 
        (myRecTypeRefBase & REF_BASE_MASK) | (recType << REC_TYPE_SHIFT);
    return(true);
}

bool GlfRecord::setRefBaseInt

(

uint8_t

refBase

)

Set the reference base from an integer value.

Parameters:

refBase

integer representation of the reference base. Int Value 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Character Base X A C M G R S V T W Y H K D B N

Returns:

true if the reference base was successfully set, false if not.

Definition at line 201 of file GlfRecord.cpp.

{
    myRecTypeRefBase = 
        (myRecTypeRefBase & REC_TYPE_MASK) | (refBase & REF_BASE_MASK);
    return(true);
}

bool GlfRecord::setRmsMapQ

(

uint8_t

rmsMapQ

)

Set the RMS of mapping qualities of reads covering the site.

Parameters:

rmsMapQ

RMS of mapping qualities

Returns:

true if successfully set, false if not.

Definition at line 243 of file GlfRecord.cpp.

{
    myRec1Base.rmsMapQ = rmsMapQ;
    myRec2Base.rmsMapQ = rmsMapQ;
    return(true);
}

bool GlfRecord::setRtypeRef

(

uint8_t

rtypeRef

)

Set the record type and reference base.

Parameters:

rtypeRef

record type & reference base. Formatted as: record_type<<4|numeric_ref_base.

Returns:

true if the record type and reference base were successfully set, false if not.

Definition at line 188 of file GlfRecord.cpp.

{
    myRecTypeRefBase = rtypeRef;
    return(true);
}

bool GlfRecord::write

(

IFILE

filePtr

)

const

Write the record to the specified file.

Parameters:

filePtr

file to write to that is in the correct position.

Returns:

true if the record was successfully written to the file, false if not.

Definition at line 113 of file GlfRecord.cpp.

References getRecordType(), and GlfStatus::INVALID.

Referenced by GlfFile::writeRecord().

{
    // TODO, split up by types of records...
    switch(getRecordType())
    {
        case 0:
            writeRtypeRef(filePtr);
            break;
        case 1:
            // write type 1.
            writeType1(filePtr);
            break;
        case 2:
            // write type 2.
            writeType2(filePtr);
            break;
        default:
            // unknown type, return error.
            String errorMsg = "Failed to write the record: unknown type: ";
            errorMsg += getRecordType();
            std::string errorString = errorMsg.c_str();
            throw(GlfException(GlfStatus::INVALID, errorString));
            return(false);
            break;
    };
    
    return(true);
}

---

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

• glf/GlfRecord.h
• glf/GlfRecord.cpp