The bamGapList class represents a list of Alignment gap (N-items in Cigar-data) sites . For each gap-site, left and right start and end positions as well as the gap-length are reported. Numbers of aligns supporting this site, number of left-sided start positions (<= 8) and the sum of overlapping nucleotides on the left side are given.
Objects from the Class
Objects can be created by calls of the form
"externalptr". Point to double linked list struct.
"data.frame". Contains bamHeader like data for stored aligns.
signature(x = "bamGapList"): Returns number of site-items in list.
signature(from = "bamGapList", to = "data.frame"): Coercion of bamGapList to data.frame.
signature("bamGapList","data.frame"): Coercion of bamGapList to data.frame.
signature(object = "bamGapList"): Prints a short message with some summarizing data.
signature(object = "bamGapList"): Returns number of aligns in specified Range.
signature(object = "bamGapList"): Returns number of align gaps in specified Range.
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