Class
BamAlignmentRecord
Represent a record from a BAM/SAM file.
Include Headers
seqan/bam_io.h
Remarks
While also used to represent SAM records, called BamAlignmentRecord since the data directly reflects a BAM record (0-based positions, identify references by ids, not names, tags stored in BAM format.)
Data Members
The position of this fragment mapping (0-based, | |
The bin of the alignment, automatically computed when writing BAM. | |
The CIGAR string as string of CigarElement objects (empty for '*'). | |
The flag of this mapping, see BamFlags for flag constants and the | |
Static member with invalid/sentinel position value. | |
Static member with invalid/sentinel position value. | |
Static member with invalid/sentinel reference id (-1 as in BAM/SAM). | |
The mapping quality (255 for '*'). | |
Position of next fragment mapping (0-based, | |
The read/query name. | |
String with Phred scores (as in SAM file, empty for '*'). | |
ID of reference for this fragment mapping (0-based, | |
ID of reference for next fragment mapping (0-based, | |
The sequence string (empty for '*'). | |
Raw BAM tag string, use BamTagsDict for comfortable access. | |
The inferred template size ( |
Member Functions
Constructor. |
Functions
Convert BamAlignmentRecord to an Align object. | |
Resets an object. | |
Returns length of BamAlignmentRecord's projection in reference. | |
Return true if a BamAlignmentRecord has the "all properly aligned" flag set. | |
Return true if a BamAlignmentRecord has the "PCR or optical duplicate" flag set. | |
Return true if a BamAlignmentRecord has the "first fragment of template" flag set. | |
Return true if a BamAlignmentRecord has the "last fragment of template" flag set. | |
Return true if a BamAlignmentRecord has the "multiple" flag set. | |
Return true if a BamAlignmentRecord has the "next fragment reverse-complemented" flag set. | |
Return true if a BamAlignmentRecord has the "next fragment unmapped" flag set. | |
Return true if a BamAlignmentRecord has the "does not pass quality controls" flag set. | |
Return true if a BamAlignmentRecord has the "reverse-complemented" flag set. | |
Return true if a BamAlignmentRecord has the "secondary alignment" flag set. | |
Return true if a BamAlignmentRecord has the "fragment unmapped" flag set. | |
reads one record (e.g. a single DNA-sequence and its meta data) from a StreamConcept, by the means of RecordReader |
See Also
SeqAn - Sequence Analysis Library - www.seqan.de