libStatGen Software 1
SamFilter Member List

This is the complete list of members for SamFilter, including all inherited members.

clipOnMismatchThreshold(SamRecord &record, GenomeSequence &refSequence, double mismatchThreshold)SamFilterstatic
CLIPPED enum valueSamFilter
FILTERED enum valueSamFilter
filterOnMismatchQuality(SamRecord &record, GenomeSequence &refSequence, uint32_t qualityThreshold, uint8_t defaultQualityInt)SamFilterstatic
filterRead(SamRecord &record)SamFilterstatic
FilterStatus enum nameSamFilter
NONE enum valueSamFilter
softClip(SamRecord &record, int32_t numFrontClips, int32_t numBackClips)SamFilterstatic
softClip(Cigar &oldCigar, int32_t numFrontClips, int32_t numBackClips, int32_t &startPos, CigarRoller &updatedCigar)SamFilterstatic
sumMismatchQuality(SamRecord &record, GenomeSequence &refSequence, uint8_t defaultQualityInt)SamFilterstatic