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983 bytes added
, 13:19, 3 August 2010
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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. |
| |- | | |- |
| | <code>void CigarRoller::getExpandedString(std::string &s)</code> | | | <code>void CigarRoller::getExpandedString(std::string &s)</code> |
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| 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. |
| + | |- |
| + | | <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 |
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| + | |
| + | === Determining the Number of Reference and Read/Query Overlaps === |