tiny-count: new edit pattern modes for the Mismatches selector

[AlexTate]

A new option will be added to tiny-count to extend the functionality of the Mismatches column of the Features Sheet. To start, the option will support two choices which describe specific edit pattern requirements that alignments must meet when they are being evaluated by rules with a mismatch requirement. When activated, these requirements apply globally to all rules with a mismatch requirement, but rules that are wildcard (blank cell, any, all, *) in this column will be unaffected, i.e., they allow for any number of mismatches regardless of the edit pattern present or required.

The two choices for this option are:

• ADAR: all mismatches must follow the A -> I edit pattern which is characteristic of the double-stranded RNA-specific adenosine deaminase (ADAR) enzyme family. Inosene is recognized as guanosine by reverse transcriptase and therefore represented as G when sequenced, so this pattern is represented as A -> G in sequencing data.
• TUT: all mismatches must follow the N -> U edit pattern at the 3' terminus which is characteristic of the Terminal Uridylyl Transferase (TUT) enzyme family. Valid mismatches must be consecutive. Reverse transcription prior to sequencing means this pattern is represented as N -> T in sequencing data.

The following is true of both counting modes:

1. The edit pattern is determined from the alignment's SEQ field and its NM and MD tags
2. Alignments to the reverse strand are evaluated for the same pattern without reverse complement
3. Insertions and deletions are both disqualifying