SAMFlags Enumeration

SAM Flags. This enum represents the bitwise flags of the SAM format.

Namespace: Bio.IO.SAM
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)

Syntax

[FlagsAttribute]
public enum SAMFlags

<FlagsAttribute>
Public Enumeration SAMFlags

[FlagsAttribute]
public enum class SAMFlags

[<FlagsAttribute>]
type SAMFlags

Members

Member name	Value	Description
PairedRead	1	0x0001 The read is paired in sequencing, no matter whether it is mapped in a pair.
MappedInProperPair	2	0x0002 The read is mapped in a proper pair (depends on the protocol, normally inferred during alignment).
UnmappedQuery	4	0x0004 The query sequence itself is unmapped.
UnmappedMate	8	0x0008 The mate is unmapped.
QueryOnReverseStrand	16	0x0010 Strand of the query (0 for forward; 1 for reverse strand).
MateOnReverseStrand	32	0x0020 Strand of the mate.
FirstReadInPair	64	0x0040 The read is the first read in a pair.
SecondReadInPair	128	0x0080 The read is the second read in a pair.
NonPrimeAlignment	256	0x0100 The alignment is not primary (a read having split hits may have multiple primary alignment records).
QualityCheckFailure	512	0x0200 The read fails platform/vendor quality checks.
Duplicate	1024	0x0400 The read is either a PCR duplicate or an optical duplicate.