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Revision as of 18:48, 7 December 2010
, 18:48, 7 December 2010no edit summary
=== Proposed Solution ===
=== Proposed Solution ===
....More details coming soon!
....More details coming soon!
==== USER API UPDATES ====
Added a class, <code>SamQuerySeqWithRef</code>, with methods <code>seqWithEquals</code> and <code>seqWithoutEquals</code>
==== Possibly useful to a User ====
Added a class, <code>SamQuerySeqWithRef</code>, with static methods <code>seqWithEquals</code> and <code>seqWithoutEquals</code>. SamRecord uses these methods to
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<source lang="cpp">
// Gets the sequence with '=' in any position where the sequence matches the reference.
// NOTE: 'N' in both the sequence and the reference is not considered a match.
// Parameters:
// currentSeq sequence that should be converted
// seq0BasedPos 0 based start position of currentSeq on the reference.
// cigar cigar string for currentSeq (used for determining how the sequence aligns to the reference)
// referenceName reference name associated with this sequence
// refSequence reference sequence object
// updatedSeq return parameter that this method sets to the current sequence, replacing any matches to the reference with '='.
void SamQuerySeqWithRef::seqWithEquals(const char * currentSeq,
int32_t seq0BasedPos,
Cigar & cigar,
const char * referenceName,
const GenomeSequence & refSequence,
std::string & updatedSeq)
// Gets the sequence converting '=' to the appropriate base using the reference.
// Parameters:
// currentSeq sequence that should be converted
// seq0BasedPos 0 based start position of currentSeq on the reference.
// cigar cigar string for currentSeq (used for determining how the sequence aligns to the reference)
// referenceName reference name associated with this sequence
// refSequence reference sequence object
// updatedSeq return parameter that this method sets to the current sequence, replacing any "=" with the base from the reference.
void SamQuerySeqWithRef::seqWithoutEquals(const char * currentSeq,
int32_t seq0BasedPos,
Cigar & cigar,
const char * referenceName,
const GenomeSequence & refSequence,
std::string & updatedSeq)
</source>
==== INTERNAL MODIFICATIONS ====
* Updated GenericSamInterface, BamInterface, and SamInterface to take TranslationType as a parameter to <code>writeRecord</code>.
** <code>SamInterface::writeRecord</code> passes the translation parameter to <code>SamRecord::getSequence</code> when it obtains the sequence to write into the SAM file.
