A pile of read alignments belonging to the same gap/contig end.
Type of the read alignment.
Type of the read alignment.
Calculates the coverage of the contigs by the given alignments. Only contigs involved in the alignments are regarded.
Returns a list of pointers to all involved alignment chains.
Get the type of the read alignment.
Returns true iff ac1 begins before ac2 on the given contig (in).
Generate basic join from read alignment.
Generate join from read alignment.
Holds a chain of local alignments that form a compound alignment. An AlignmentChain should contain at least one element.
Alignment of a read against the reference. This is either one or two alignment chains which belong to the same read and one or two reference contig(s).
An alignment chain with a "seed", ie. hint for it's intended location.
Everything to handle local alignments and friends.