Difference between revisions of "SAM/BAM Convert Sequence"
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Jump to navigationJump to search (Created page with '== SAM/BAM support conversion between '=' and the base in a sequence == '''Request:''' To be able to call SamRecord::getSequence and have it return the sequence with '=' or with…') |
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=== 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 | ||
<p> | <p> | ||
| + | <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. | ||
Revision as of 18:48, 7 December 2010
SAM/BAM support conversion between '=' and the base in a sequence
Request: To be able to call SamRecord::getSequence and have it return the sequence with '=' or with the correct bases.
Requester: Goncalo Abecasis & Hyun Min Kang
Date Requested: Nov 23, 2010?
Notes
It was requested to have this handled within the getSequence call so the user doesn't have to convert the sequence after calling getSequence.
Proposed Solution
....More details coming soon!
USER API UPDATES
Possibly useful to a User
Added a class, SamQuerySeqWithRef, with static methods seqWithEquals and seqWithoutEquals. SamRecord uses these methods to
// 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)
INTERNAL MODIFICATIONS
- Updated GenericSamInterface, BamInterface, and SamInterface to take TranslationType as a parameter to
writeRecord.SamInterface::writeRecordpasses the translation parameter toSamRecord::getSequencewhen it obtains the sequence to write into the SAM file.
