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| <code>const char * CigarRoller::getString()</code>
| <code>const char * CigarRoller::getString()</code>
| REturns the string representation of this CIGAR object.
| Returns the string representation of this CIGAR object.
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| <code>void CigarRoller::getExpandedString(std::string &s)</code>
| <code>void CigarRoller::getExpandedString(std::string &s)</code>
See [[C++ Class: CigarRoller#Mapping Between Reference and Read/Query|Mapping Between Reference and Read/Query]] for a more detailed explanation with examples as to how it works.
See [[C++ Class: CigarRoller#Mapping Between Reference and Read/Query|Mapping Between Reference and Read/Query]] for a more detailed explanation with examples as to how it works.
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| <code>uint32_t getNumOverlaps(int32_t start, int32_t end, int32_t queryStartPos)</code>
| Return the number of bases that overlap the reference and the read associated with this cigar that falls within the specified region.
start : inclusive start position (reference position) of the region to check for overlaps in. (-1 indicates to start at the beginning of the reference.)
end : exclusive end position (reference position) of the region to check for overlaps in. (-1 indicates to go to the end of the reference.)
queryStartPos : leftmost mapping position of the first matching base in the query.
NOTE: ensure that start, end, and queryStartPos are all in the same base (0 or 1).
See [[C++ Class: CigarRoller#Determining the Number of Reference and Read/Query Overlaps|Determining the Number of Reference and Read/Query Overlaps]] for a more detailed explanation with examples as to how it works.
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refPosition:5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32(and any value over 32)
refPosition:5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32(and any value over 32)
Return: 0 1 2 3 NA NA NA NA NA NA NA NA NA NA 4 5 6 7 11 12 NA NA NA NA 13 14 15 NA
Return: 0 1 2 3 NA NA NA NA NA NA NA NA NA NA 4 5 6 7 11 12 NA NA NA NA 13 14 15 NA
=== Determining the Number of Reference and Read/Query Overlaps ===
