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| <code>int32_t CigarRoller::getQueryIndex(int32_t refOffset)</code>
| <code>int32_t CigarRoller::getQueryIndex(int32_t refOffset)</code>
| Return the query index associated with the specified reference offset or INDEX_NA based on this cigar.
| Return the query index associated with the specified reference offset or INDEX_NA based on this cigar.
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>int32_t CigarRoller::getRefPosition(int32_t queryIndex, int32_t queryStartPos)</code>
|Return the reference position associated with the specified query index or INDEX_NA based on this cigar and the specified queryStartPos.
queryStartPops is the leftmost mapping position of the first matching base in the query.
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.
|-
| <code>int32_t CigarRoller::getQueryIndex(int32_t refPosition, int32_t queryStartPos)</code>
| Return the query index associated with the specified reference position and queryStartPos or INDEX_NA based on this cigar.
queryStartPops is the leftmost mapping position of the first matching base in the query.
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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