tiny-count: new selector: Mismatches

[AlexTate]

This PR introduces a new selector for tiny-count: Mismatches. It is used for placing constraints on the edit distance between an alignment and the reference, and it is evaluated in Stage 2 after the Overlap selector. Users can specify ranges, lists, wildcards, and single values in this column.

Edit distance is determined from:

• The NM tag, if present
• The CIGAR string (I, D, and X operations) if the NM tag is not present in the first alignment
• If the NM tag is present in the first alignment but missing from a subsequent alignment, then the subsequent alignment's edit distance assumes a default value of zero

The former function for producing alignment dictionaries, SAM_reader._parse_alignments(), has been converted to a standalone Cython class which utilizes pysam's Cython API. As a result, runtimes appear to be negligibly affected (~4-5% slower) rather than the 20-30% reduction measured while using pysam's Python API. This dedicated class is also responsible for accumulating alignments for decollapsed outputs, but delegates all other decollapsing responsibility to the Python-space SAM_reader class. I've made an effort to minimize the Cython surface area due to its complications with debugging.

Additionally:

• The first sequence in each alignment file is checked to make sure that it contains the read sequence (error otherwise)
• If the user elects to have decollapsed outputs produced, alignments are accumulated as pysam's AlignedSegmet objects rather than alignment dictionaries because they have a significantly smaller memory footprint
• The column order of the Features Sheet (specifically the Overlap column) has been updated to match the order shown in the selection diagram

Closes #296

[taimontgomery]

Tested with ram1 data and 0, 1, or 3 mutations introduced into the genome fa and using Mismatch selector.