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incorrect handling of "D" in existing CIGAR strings with mask_* functions

5

Here's an example: `print("3M1D137M",cigar.Cigar("3M1D137M").mask_left(4).cigar)` Which will yield: > 3M1D137M 5S136M Which is incorrect, as the original "3M1D137M" string has query sequence length 140, but the left-masked query sequence length of...

ahstram

Correct handling of "D" in mask_left(), with new merge_softclipped_* functions

1

Correct handling of "D" in mask_left(), with new merge_softclipped_deletions() and merge_softclipped_insertions() functions to ensure "S" operations are not immediately followed by "D", "N", "I" or "P" This should address issue...

ahstram