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