CigarRoller Proposed Update - Revision history

Mktrost at 15:11, 4 August 2010

2010-08-04T15:11:13Z

← Older revision		Revision as of 11:11, 4 August 2010
Line 30:		Line 30:
	\| <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???
	\|-		\|-
	\|		\|

Mktrost: /* How would this be used by SamRecord */

2010-08-04T15:03:08Z

How would this be used by SamRecord

← Older revision		Revision as of 11:03, 4 August 2010
Line 105:		Line 105:
	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.		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 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.

Mktrost at 15:00, 4 August 2010

2010-08-04T15:00:08Z

@@ Line 47: / Line 47: @@
 | <code>void CigarRoller::getExpandedString(std::string &s)</code>
 | <code>void Cigar::getExpandedString(std::string &s)</code>
 |-
 | <code>void CigarRoller::clear()</code>
@@ Line 93: / Line 101: @@
 Should this be its own class?

Mktrost: Created page with '* Should we rename CigarRoller to Cigar? * Should we be consistent in upper-case vs lower-case first letter of method names? * Should Cigar require a start position? ** I would l…'

2010-08-04T14:52:16Z

Created page with '* Should we rename CigarRoller to Cigar? * Should we be consistent in upper-case vs lower-case first letter of method names? * Should Cigar require a start position? ** I would l…'

New page

* Should we rename CigarRoller to Cigar?
* Should we be consistent in upper-case vs lower-case first letter of method names?
* Should Cigar require a start position?
** I would lean to say no and it just gets passed in when doing things based on positions. That way it can change external to this and really it isn't necessary for the cigar.

== Public ==
=== Public Methods ===
{| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
|-style="background: #f2f2f2; text-align: center;"
! Current Methods !! Proposed Methods !! Notes
|-
| <code>CigarRoller::CigarRoller()</code>
| <code>Cigar::Cigar()</code>
|-
| <code>CigarRoller::CigarRoller(const char *cigarString)</code>
| <code>Cigar::Cigar(const char *cigarString)</code>
|-
|
| <code>Cigar::Cigar(const uint32_t *cigarBuffer, uint16_t cigarBufferLength)</code>
|-
| <code>CigarRoller & CigarRoller::operator += (CigarRoller &rhs)</code>
| <code>Cigar & Cigar::operator += (Cigar &rhs)</code>
|-
| <code>CigarRoller & CigarRoller::operator += (CigarOperator &rhs)</code>
| <code>Cigar & Cigar::operator += (CigarOperator &rhs)</code>
|-
| <code>void CigarRoller::Add(Operation operation, int count)</code>
| <code>void Cigar::add(Operation operation, int count)</code>
|-
| <code>void CigarRoller::Add(const char *cigarString)</code>
| <code>void Cigar::add(const char *cigarString)</code>
|-
|
| <code>void Cigar::add(const uint32_t *cigarBuffer, uint16_t cigarBufferLength)</code>
| Does it make sense to add a buffer?
|-
| <code>void CigarRoller::Set(const char *cigarString)</code>
| <code>void Cigar::set(const char *cigarString)</code>
|-
|
| <code>void Cigar::set(const uint32_t *cigarBuffer, uint16_t cigarBufferLength)</code>
|-
| <code>const char * CigarRoller::getString()</code>
| <code>const char * Cigar::getString()</code>
| Currently user must delete the const char* do we want that? How to handle? Would it be better to pass in a std::string&?
|-
| <code>void CigarRoller::getExpandedString(std::string &s)</code>
| <code>void Cigar::getExpandedString(std::string &s)</code>
|-
| <code>void CigarRoller::clear()</code>
| <code>void Cigar::clear()</code>
|-
| <code>CigarOperator & CigarRoller::operator [] (int i)</code>
| <code>CigarOperator & Cigar::operator [] (int i)</code>
|-
| <code>bool CigarRoller::operator == (CigarRoller &rhs)</code>
| <code>bool Cigar::operator == (CigarRoller &rhs)</code>
| What is this for?
|-
| <code>int CigarRoller::size()</code>
| <code>int CigarRoller::getNumOperations()</code>
| I find "size" confusing - is it the number of operations, the sum of the op lengths, etc.
|-
| <code>void CigarRoller::Dump()</code>
| <code>void CigarRoller::dump()</code>
|-
| <code>int CigarRoller::getExpectedQueryBaseCount()</code>
| <code>int Cigar::getNumQueryBases()</code>
| Returns the expected read length
|-
| <code>int CigarRoller::getExpectedReferenceBaseCount()</code>
| <code>int Cigar::getNumRefBases()</code>
| Return how many bases in the reference are spanned by the given CIGAR string
|-
| <code>int32_t CigarRoller::getRefOffset(int32_t queryIndex)</code>
| <code>int32_t Cigar::getRefOffset(int32_t queryIndex)</code>
|-
| <code>int32_t CigarRoller::getQueryIndex(int32_t refOffset)</code>
| <code>int32_t Cigar::getQueryIndex(int32_t refOffset)</code>
|-
| <code>int32_t CigarRoller::getRefPosition(int32_t queryIndex, int32_t queryStartPos)</code>
| <code>int32_t Cigar::getRefPosition(int32_t queryIndex, int32_t queryStartPos)</code>
|-
| <code>int32_t CigarRoller::getQueryIndex(int32_t refPosition, int32_t queryStartPos)</code>
| <code>int32_t Cigar::getQueryIndex(int32_t refPosition, int32_t queryStartPos)</code>
|-
| <code>uint32_t CigarRoller::getNumOverlaps(int32_t start, int32_t end, int32_t queryStartPos)</code>
| <code>uint32_t Cigar::getNumOverlaps(int32_t start, int32_t end, int32_t queryStartPos)</code>
|}

=== Public Member Data ===
CigarOperator struct

Should this be its own class?