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Jump to navigationJump to searchCigarRoller Proposed Update (view source)
Revision as of 11:11, 4 August 2010
, 11:11, 4 August 2010no edit summary
| <code>void CigarRoller::Add(const char *cigarString)</code>
| <code>void CigarRoller::Add(const char *cigarString)</code>
| <code>void Cigar::add(const char *cigarString)</code>
| <code>void Cigar::add(const char *cigarString)</code>
| What happens if an invalid character is found while parsing this???
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| <code>void CigarRoller::getExpandedString(std::string &s)</code>
| <code>void CigarRoller::getExpandedString(std::string &s)</code>
| <code>void Cigar::getExpandedString(std::string &s)</code>
| <code>void Cigar::getExpandedString(std::string &s)</code>
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| <code>uint16_t Cigar::getBufferSize(uint32_t *cigarBuffer, uint16_t cigarBufferLength)</code>
| Length the buffer would need to be.
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| <code>void Cigar::getBuffer(uint32_t *cigarBuffer)</code>
| Assumes the user properly allocated a buffer of getBufferSize - is there a better what to do this? I think there is, but I'm drawing a blank.
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| <code>void CigarRoller::clear()</code>
| <code>void CigarRoller::clear()</code>
Should this be its own class?
Should this be its own class?
== How would this be used by SamRecord ==
When SamRecord needs to convert from SAM to BAM or BAM to SAM or needs alignment length or numOverlaps,e tc, it would use the appropriate Cigar::set.
The conversion logic and parsing logic SAM & BAM would only be located in this Cigar class.
The alignment length calculation would come from the cigar.
What about alignment end (pass in the start position)?
Unclipped Start/End would also be from Cigar - or would it just be offsets - or either depending on whether or not the start pos is passed in.
