ReadAlignment

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).

struct ReadAlignment {

SeededAlignment[2] _alignments;

size_t _length;

bool isInOrder [@property getter];

bool isValid [@property getter];

ReadAlignmentType type [@property getter];

bool isExtension [@property getter];

bool isFrontExtension [@property getter];

bool isBackExtension [@property getter];

bool isGap [@property getter];

bool isParallel [@property getter];

bool isAntiParallel [@property getter];

}

Members

Properties

isAntiParallel bool isAntiParallel [@property getter]: Returns true iff the read alignment spans a gap and the flanking contigs have in different orientation (according to this alignment).
isBackExtension bool isBackExtension [@property getter]: Returns true iff the read alignment is an back extension, ie. it is an extension and reaches over the back of the reference contig.
isExtension bool isExtension [@property getter]: Returns true iff the read alignment is an extension, ie. it is a front or back extension.
isFrontExtension bool isFrontExtension [@property getter]: Returns true iff the read alignment is an front extension, ie. it is an extension and reaches over the front of the reference contig.
isGap bool isGap [@property getter]: Returns true iff the read alignment spans a gap, ie. two alignments of the same read on different reference contigs are involved.
isInOrder bool isInOrder [@property getter]: If readAlignment is a gap return true iff the first alignment's contigA.id is lower than the second alignment's; otherwise returns true.
isParallel bool isParallel [@property getter]: Returns true iff the read alignment spans a gap and the flanking contigs have in the same orientation (according to this alignment).
isValid bool isValid [@property getter]: Returns true iff the read alignment is valid, ie. it is either an extension or gap.
type ReadAlignmentType type [@property getter]: Get the type of the read alignment.

ReadAlignment

Members

Properties

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