A single read alignment with mandatory and optional fields that can be contained in a SAM file alignment line.
See http://samtools.github.io/hts-specs/SAMv1.pdf - Sections 1.4 and 1.5.
The struct sam-alignment has a default constructor make-sam-alignment.
Accessor sam-alignment-qname of type base-string refers to the Query template NAME.
Accessor sam-alignment-flag of type fixnum refers to the bitwise FLAG.
Accessor sam-alignment-rname of type base-string refers to the Reference sequence NAME.
Accessor sam-alignment-pos of type int32 refers to the 1-based leftmost mapping POSition.
Accessor sam-alignment-mapq of type fixnum refers to the MAPping quality.
Accessor sam-alignment-cigar of type base-string refers to the CIGAR string.
Accessor sam-alignment-rnext of type base-string refers to the Reference sequence name of the mate/NEXT read.
Accessor sam-alignment-pnext of type int32 refers to the 1-based leftmost mapping Position of the mate/NEXT read.
Accessor sam-alignment-tlen of type int32 refers to the observed Template LENgth.
Accessor sam-alignment-seq of type base-string refers to the segment SEQuence.
Accessor sam-alignment-qual of type base-string refers to the ASCII of Phred-scaled base QUALity+33.
Accessor sam-alignment-tags of type property list refers to the optional fields in a read alignment.
Accessor sam-alignment-temps of type property list refers to additional optional fields not stored in any storage format, but reserved for temporary values in filters.