AlignmentChain

Holds a chain of local alignments that form a compound alignment. An AlignmentChain should contain at least one element.

struct AlignmentChain {

enum maxScore;

enum emptyFlags;

id_t id;

Contig contigA;

Contig contigB;

Flags flags;

LocalAlignment[] localAlignments;

trace_point_t tracePointDistance;

coord_t traceLength;

coord_t traceDiffs;

}

Members

isFullyContained bool isFullyContained(): Returns true if the aligned read contigB (with extensions on either end) is fully contained in the reference contigA.

isProper bool isProper [@property getter]: This alignment is called proper iff it starts and ends at a read boundary.