Gets bin depending on POS and CIGAR values.

Extended CIGAR string.

SAM flags. SAMFlags

Is this read a special dummy read? These read types are a special type in later BAM file formats that are designed to hold annotation data. They are identified as having SEQ set to *, FLAG bits 0x100 and 0x200 set (secondary and filtered), and a CT tag.

Inferred insert size.

Mapping quality (phred-scaled posterior probability that the mapping position of this read is incorrect).

Metadata of this aligned sequence. SAMAlignedSequenceHeader is stored with the key "SAMAlignedSequenceHeader".

One-based leftmost mate position of the clipped sequence.

Mate reference sequence name.

Optional fields.

One-based leftmost position/coordinate of the clipped sequence.

Query pair name if paired; or Query name if unpaired.

Gets or sets read/query/aligned sequence.

Gets one based alignment end position of reference sequence depending on CIGAR Value.

Reference sequence name.

Always returns QuerySequence in a list.