Cigar Class Reference

Inheritance diagram for Cigar:

[legend]

Collaboration diagram for Cigar:

[legend]

List of all members.

Classes
struct	CigarOperator
Public Types
enum	Operation {   none, match, mismatch, insert,   del, skip, softClip, hardClip,   pad }
Public Member Functions
void	getCigarString (String &cigarString) const
void	getCigarString (std::string &cigarString) const
void	getExpandedString (std::string &s) const
	obtain a non-run length encoded string of operations
const CigarOperator &	operator[] (int i) const
const CigarOperator &	getOperator (int i) const
bool	operator== (Cigar &rhs) const
int	size () const
void	Dump () const
int	getExpectedQueryBaseCount () const
	return the length of the read that corresponds to the current CIGAR string.
int	getExpectedReferenceBaseCount () const
	return the number of bases in the reference that this read "spans"
int	getNumBeginClips () const
	Return the number of clips that are at the beginning of the cigar.
int	getNumEndClips () const
	Return the number of clips that are at the end of the cigar.
int32_t	getRefOffset (int32_t queryIndex)
int32_t	getQueryIndex (int32_t refOffset)
int32_t	getRefPosition (int32_t queryIndex, int32_t queryStartPos)
int32_t	getQueryIndex (int32_t refPosition, int32_t queryStartPos)
uint32_t	getNumOverlaps (int32_t start, int32_t end, int32_t queryStartPos)
Static Public Member Functions
static bool	foundInQuery (Operation op)
static bool	isClip (Operation op)
Static Public Attributes
static const int32_t	INDEX_NA = -1
Protected Member Functions
void	clearQueryAndReferenceIndexes ()
void	setQueryAndReferenceIndexes ()
Protected Attributes
std::vector< CigarOperator >	cigarOperations
Friends
std::ostream &	operator<< (std::ostream &stream, const Cigar &cigar)

---

Detailed Description

Definition at line 80 of file Cigar.h.

---

Member Function Documentation

void Cigar::getExpandedString

(

std::string &

s

)

const

obtain a non-run length encoded string of operations

The returned string is actually also a valid CIGAR string, but it does not have any digits in it - only the characters themselves. In theory this makes it easier to parse some reads.

/return s the string to populate

Definition at line 63 of file Cigar.cpp.

{
    s = "";

    std::vector<CigarOperator>::const_iterator i;

    // Progressively append the character representations of the operations to
    // the string passed in

    for (i = cigarOperations.begin(); i != cigarOperations.end(); i++)
    {
        for (uint32_t j = 0; j<(*i).count; j++) s += (*i).getChar();
    }
    return;
}

int Cigar::getExpectedQueryBaseCount

(

)

const

return the length of the read that corresponds to the current CIGAR string.

For validation, we should expect that a sequence read in a SAM file will be the same length as the value returned by this method.

Example: 3M2D3M describes a read with three bases matching the reference, then skips 2 bases, then has three more bases that match the reference (match/mismatch). In this case, the read length is expected to be 6.

Example: 3M2I3M describes a read with 3 match/mismatch bases, two extra bases, and then 3 more match/mistmatch bases. The total in this example is 8 bases.

/return returns the expected read length

Definition at line 110 of file Cigar.cpp.

{
    int matchCount = 0;
    std::vector<CigarOperator>::const_iterator i;
    for (i = cigarOperations.begin(); i != cigarOperations.end(); i++)
    {
        switch (i->operation)
        {
            case match:
            case mismatch:
            case softClip:
            case insert:
                matchCount += i->count;
                break;
            default:
                // we only care about operations that are in the query sequence.
                break;
        }
    }
    return matchCount;
}

int Cigar::getExpectedReferenceBaseCount

(

)

const

return the number of bases in the reference that this read "spans"

When doing range checking, we occassionally need to know how many total bases the CIGAR string represents as compared to the reference.

Examples: 3M2D3M describes a read that overlays 8 bases in the reference. 3M2I3M describes a read with 3 bases that match the reference, two additional bases that aren't in the reference, and 3 more bases that match the reference, so it spans 6 bases in the reference.

/return how many bases in the reference are spanned by the given CIGAR string

Definition at line 149 of file Cigar.cpp.

{
    int matchCount = 0;
    std::vector<CigarOperator>::const_iterator i;
    for (i = cigarOperations.begin(); i != cigarOperations.end(); i++)
    {
        switch (i->operation)
        {
            case match:
            case mismatch:
            case del:
            case skip:
                matchCount += i->count;
                break;
            default:
                // we only care about operations that are in the reference sequence.
                break;
        }
    }
    return matchCount;
}

---

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

• lib/general/Cigar.h
• lib/general/Cigar.cpp