Module mate_fix 

Check for mate fixing.

The strategy here is as follows:

• Always check first for the user-based filter status of each mate, if one fails, go with the other mate, if both fail, default to a
• Try one of the MateResolutionStrategy variants

MateResolutionStrategy::BaseQualMapQualFirstInPair

If either is deletion / ref skip -> MAPQ -> first in pair Else BASEQ -> MAPQ -> first in pair

MateResolutionStrategy::BaseQualMapQualIUPAC

If either is deletion / ref skip -> MAPQ -> first in pair Else BASEQ -> MAPQ -> IAUPAC

MateResolutionStrategy::BaseQualMapQualN

If either is deletion / ref skip -> MAPQ -> first in pair Else BASEQ -> MAPQ -> N (if ambiguous)

MateResolutionStrategy::MapQualBaseQualFirstInPair

If either is deletion / ref skip -> MAPQ -> first in pair Else MAPQ -> BASEQ-> first in pair

MateResolutionStrategy::MapQualBaseQualIUPAC

If either is deletion / ref skip -> MAPQ -> first in pair Else MAPQ -> BASEQ -> IUPAC

MateResolutionStrategy::MapQualBaseQualN

If either is deletion / ref skip -> MAPQ -> first in pair Else MAPQ -> BASEQ -> N (if ambiguous)

MateResolutionStrategy::IUPAC

If either is deletion / ref skip -> MAPQ -> first in pair Else IUPAC

MateResolutionStrategy::N

If either is deletion / ref skip -> MAPQ -> first in pair Else N

MateResolutionStrategy::Original

MAPQ -> first in pair

Structs

MateResolution

Result of mate resolution comparison containing ordering and optional base recommendation.

Enums

Base

IUPAC Bases

MateResolutionStrategy

Strategies for resolving which mate to use when overlapping mates disagree on a base call.