18 #ifndef __CIGAR_HELPER_H__
19 #define __CIGAR_HELPER_H__
21 #include "SamRecord.h"
27 static const int32_t NO_CLIP = -1;
42 int32_t refPosition0Based,
44 int32_t &new0BasedPosition);
60 int32_t refPosition0Based,
Class for helping to filter a SAM/BAM record.
static int32_t softClipBeginByRefPos(SamRecord &record, int32_t refPosition0Based, CigarRoller &newCigar, int32_t &new0BasedPosition)
Soft clip the cigar from the beginning of the read at the specified reference position.
static int32_t softClipEndByRefPos(SamRecord &record, int32_t refPosition0Based, CigarRoller &newCigar)
Soft clip the cigar from the back of the read at the specified reference position.
The purpose of this class is to provide accessors for setting, updating, modifying the CIGAR object....
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record.