90a1f5e15c
* When hard clipping a read that had insertions in it, the insertion was being added to the cigar string's hard clip element. This way, the old UnclippedStart() was being modified and so was the calculation of the new AlignmentStart(). Fixed it by subtracting the number of insertions clipped from the total number of hard clipped bases. * Walker was sending read instead of filtered read when deleting a read that contains only Q2 bases * Sliding the window was causing reads that started on the new start position to be entirely clipped. |
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