- void SetIsDuplicate(bool ok); // sets value of "PCR duplicate" flag
- void SetIsFailedQC(bool ok); // sets value of "failed quality control" flag
- void SetIsFirstMate(bool ok); // sets value of "alignment is first mate" flag
- void SetIsMapped(bool ok); // sets value of "alignment is mapped" flag
- void SetIsMateMapped(bool ok); // sets value of "alignment's mate is mapped" flag
- void SetIsMateReverseStrand(bool ok); // sets value of "alignment's mate mapped to reverse strand" flag
- void SetIsPaired(bool ok); // sets value of "alignment part of paired-end read" flag
- void SetIsPrimaryAlignment(bool ok); // sets value of "position is primary alignment" flag
- void SetIsProperPair(bool ok); // sets value of "alignment is part of read that satisfied paired-end resolution" flag
- void SetIsReverseStrand(bool ok); // sets value of "alignment mapped to reverse strand" flag
- void SetIsSecondMate(bool ok); // sets value of "alignment is second mate on read" flag
-
- // legacy methods (consider deprecated, but still available)
- void SetIsMateUnmapped(bool ok); // complement of using SetIsMateMapped()
- void SetIsSecondaryAlignment(bool ok); // complement of using SetIsPrimaryAlignment()
- void SetIsUnmapped(bool ok); // complement of using SetIsMapped()
+ void SetIsDuplicate(bool ok); // sets value of "PCR duplicate" flag
+ void SetIsFailedQC(bool ok); // sets value of "failed quality control" flag
+ void SetIsFirstMate(bool ok); // sets value of "alignment is first mate" flag
+ void SetIsMapped(bool ok); // sets value of "alignment is mapped" flag
+ void SetIsMateMapped(bool ok); // sets value of "alignment's mate is mapped" flag
+ void SetIsMateReverseStrand(bool ok); // sets value of "alignment's mate mapped to reverse strand" flag
+ void SetIsPaired(bool ok); // sets value of "alignment part of paired-end read" flag
+ void SetIsPrimaryAlignment(bool ok); // sets value of "position is primary alignment" flag
+ void SetIsProperPair(bool ok); // sets value of "alignment is part of read that satisfied paired-end resolution" flag
+ void SetIsReverseStrand(bool ok); // sets value of "alignment mapped to reverse strand" flag
+ void SetIsSecondMate(bool ok); // sets value of "alignment is second mate on read" flag