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
binThe bin of the alignment, automatically computed when writing BAM.
cigarThe CIGAR string as string of CigarElement objects (empty for '*').
flagThe flag of this mapping, see BamFlags for flag constants and the hasFlag* functions.
INVALID_LENStatic member with invalid/sentinel position value.
INVALID_POSStatic member with invalid/sentinel position value.
INVALID_REFIDStatic member with invalid/sentinel reference id (-1 as in BAM/SAM).
mapQThe mapping quality (255 for '*').
pNextPosition of next fragment mapping (0-based, INVALID_POS for '*')
posThe position of this fragment mapping (0-based, INVALID_POS for '*').
qNameThe read/query name.
qualString with Phred scores (as in SAM file, empty for '*').
rIdID of reference for this fragment mapping (0-based, INVALID_REFID for '*').
rNextIdID of reference for next fragment mapping (0-based, INVALID_REFID for '*')
seqThe sequence string (empty for '*').
tagsRaw BAM tag string, use BamTagsDict for comfortable access.
tLenThe inferred template size (INVALID_LEN for '*')
Member Functions
BamAlignmentRecordConstructor.
Functions
bamRecordToAlignmentConvert BamAlignmentRecord to an Align object.
clearResets an object.
getAlignmentLengthInRefReturns length of BamAlignmentRecord's projection in reference.
hasFlagAllProperReturn true if a BamAlignmentRecord has the "all properly aligned" flag set.
hasFlagDuplicateReturn true if a BamAlignmentRecord has the "PCR or optical duplicate" flag set.
hasFlagFirstReturn true if a BamAlignmentRecord has the "first fragment of template" flag set.
hasFlagLastReturn true if a BamAlignmentRecord has the "last fragment of template" flag set.
hasFlagMultipleReturn true if a BamAlignmentRecord has the "multiple" flag set.
hasFlagNextRCReturn true if a BamAlignmentRecord has the "next fragment reverse-complemented" flag set.
hasFlagNextUnmappedReturn true if a BamAlignmentRecord has the "next fragment unmapped" flag set.
hasFlagQCNoPassReturn true if a BamAlignmentRecord has the "does not pass quality controls" flag set.
hasFlagRCReturn true if a BamAlignmentRecord has the "reverse-complemented" flag set.
hasFlagSecondaryReturn true if a BamAlignmentRecord has the "secondary alignment" flag set.
hasFlagUnmappedReturn true if a BamAlignmentRecord has the "fragment unmapped" flag set.
readRecordreads one record (e.g. a single DNA-sequence and its meta data) from a Stream, by the means of RecordReader Read Lastz "general" format record.
See Also
SeqAn - Sequence Analysis Library - www.seqan.de
 

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