Rerrrt: Examine RT error rates through sequencing.

The heavy lifting of locating reads which are/not identical to the template was performed by errrt.pm and returns a series of compressed tables of identical read ids and non-identical insertions, deletions, and mismatches. This function is intended to read those two files, gather the resulting data, and make some sense of it.

quantify_parsed(
  changed = NULL,
  identical = NULL,
  min_reads = NULL,
  min_indexes = NULL,
  min_sequencer = 10,
  prune_n = TRUE,
  min_position = 24,
  max_position = 176,
  max_mutations_per_read = NULL,
  reencode = FALSE,
  verbose = TRUE
)

`changed`	File containing the set of changed reads/indexes, by default named 'step4.txt.xz' by errrt.pm.
`identical`	File containing the set of identical reads/indexes, by default named 'step2_identical_reads.txt.xz' by errrt.pm.
`min_reads`	Minimum number of reads for each index required to include each index in the final result.
`min_indexes`	Minimum number of indexes required to include a given mutation in the final result.
`min_sequencer`	Minimum number of total reads to consider an index as associated with a sequencer-based error.
`prune_n`	Remove mutations of a base to 'N'?
`min_position`	Filter mutations before this position?
`max_position`	Filter mutations after this position?
`max_mutations_per_read`	If a read has more than this number of mutations, drop it.
`reencode`	Rewrite the indexes on a different scale to save memory (6 bit instead of 2)
`verbose`	Print information describing what is happening while this runs.