JAL-2742: Out by one error in CigarArray constructor
|Participant||Role||Time Spent||Comments||Latest Comment|
|Author||21m||3||I've removed getViewAsCigars. Remainder seems a rather la...|
|Reviewer - Complete||23m||12||You reach it from AlignmentView constructor when there ar...|
The CigarArray constructor builds a CigarArray based on a selection group and a set of hidden columns: hidden columns within the bounds of the selection group are marked as D.
However if the selection group starts at the same column as a hidden columns region ends i.e. overlap of 1 column, the CIGAR string is created as if the column were not hidden. E.g.
selection group = [6,23]
hidden columns = [3,6],[16,20]
resulting CIGAR string: 10M5D3M (should be 1D9M5D3M)
selection groups starting earlier give expected results of:
selection group = [5,23] : CIGAR = 2D9M5D3M
selection group = [4,23] : CIGAR = 3D9M5D3M
selection group = [3,23] : CIGAR = 4D9M5D3M
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