BamAlignmentRecord

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

beginPos	The position of this fragment mapping (0-based, INVALID_POS for '*').
bin	The bin of the alignment, automatically computed when writing BAM.
cigar	The CIGAR string as string of CigarElement objects (empty for '*').
flag	The flag of this mapping, see BamFlags for flag constants and the hasFlag* functions.
INVALID_LEN	Static member with invalid/sentinel position value.
INVALID_POS	Static member with invalid/sentinel position value.
INVALID_REFID	Static member with invalid/sentinel reference id (-1 as in BAM/SAM).
mapQ	The mapping quality (255 for '*').
pNext	Position of next fragment mapping (0-based, INVALID_POS for '*')
qName	The read/query name.
qual	String with Phred scores (as in SAM file, empty for '*').
rID	ID of reference for this fragment mapping (0-based, INVALID_REFID for '*').
rNextId	ID of reference for next fragment mapping (0-based, INVALID_REFID for '*')
seq	The sequence string (empty for '*').
tags	Raw BAM tag string, use BamTagsDict for comfortable access.
tLen	The inferred template size (INVALID_LEN for '*')

Member Functions

BamAlignmentRecord

Constructor.

Functions

bamRecordToAlignment	Convert BamAlignmentRecord to an Align object.
clear	Resets an object.
getAlignmentLengthInRef	Returns length of BamAlignmentRecord's projection in reference.
hasFlagAllProper	Return true if a BamAlignmentRecord has the "all properly aligned" flag set.
hasFlagDuplicate	Return true if a BamAlignmentRecord has the "PCR or optical duplicate" flag set.
hasFlagFirst	Return true if a BamAlignmentRecord has the "first fragment of template" flag set.
hasFlagLast	Return true if a BamAlignmentRecord has the "last fragment of template" flag set.
hasFlagMultiple	Return true if a BamAlignmentRecord has the "multiple" flag set.
hasFlagNextRC	Return true if a BamAlignmentRecord has the "next fragment reverse-complemented" flag set.
hasFlagNextUnmapped	Return true if a BamAlignmentRecord has the "next fragment unmapped" flag set.
hasFlagQCNoPass	Return true if a BamAlignmentRecord has the "does not pass quality controls" flag set.
hasFlagRC	Return true if a BamAlignmentRecord has the "reverse-complemented" flag set.
hasFlagSecondary	Return true if a BamAlignmentRecord has the "secondary alignment" flag set.
hasFlagUnmapped	Return true if a BamAlignmentRecord has the "fragment unmapped" flag set.
readRecord	reads one record (e.g. a single DNA-sequence and its meta data) from a StreamConcept, by the means of RecordReader