18 #ifndef __SAM_FILTER_H__
19 #define __SAM_FILTER_H__
21 #include "SamRecord.h"
22 #include "GenomeSequence.h"
43 double mismatchThreshold);
54 int32_t numFrontClips,
55 int32_t numBackClips);
72 int32_t numFrontClips,
84 uint32_t qualityThreshold,
85 uint8_t defaultQualityInt);
95 uint8_t defaultQualityInt);
static void filterRead(SamRecord &record)
Filter the read by marking it as unmapped.
This class represents the CIGAR without any methods to set the cigar (see CigarRoller for that).
@ CLIPPED
Filtering clipped the read.
Create/Access/Modify/Load Genome Sequences stored as binary mapped files.
@ NONE
The filter did not affect the read.
@ FILTERED
Filtering caused the read to be modified to unmapped.
Class for helping to filter a SAM/BAM record.
FilterStatus
Enum describing what sort of filtering was done.
static uint32_t sumMismatchQuality(SamRecord &record, GenomeSequence &refSequence, uint8_t defaultQualityInt)
Get the sum of the qualities of all mismatches in the record.
static FilterStatus clipOnMismatchThreshold(SamRecord &record, GenomeSequence &refSequence, double mismatchThreshold)
Clip the read based on the specified mismatch threshold.
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record.
The purpose of this class is to provide accessors for setting, updating, modifying the CIGAR object....
static FilterStatus filterOnMismatchQuality(SamRecord &record, GenomeSequence &refSequence, uint32_t qualityThreshold, uint8_t defaultQualityInt)
Filter the read based on the specified quality threshold.
static FilterStatus softClip(SamRecord &record, int32_t numFrontClips, int32_t numBackClips)
Soft clip the record from the front and/or the back.