tiny-count: option for normalization by genomic hits, improvements in stats collection precision

[AlexTate]

The two normalization-by-hits options, by genomic hits and feature hits, can now be disabled both independently and in tandem. When either normalization step is disabled, two new stats are reported in summary stats in place of Mapped Reads:

• Non-normalized Mapped Reads: the sum of assigned and unassigned reads according to the normalization config
• Normalized Mapped Reads: the true read count

tiny-plot automatically uses the appropriate stat for calculating proportions in rule_charts and class_charts.

Internal Consistency Checks for Reported Stats

The counts reported in all output stats files are now thoroughly checked for internal consistency. Discrepancies are reported to console with a clear description rather than being treated as an error. If alignment stats and summary stats have internal disagreement, a checksum table is produced as a CSV file for further diagnosis. Care has been taken to ensure that the consistency checker can fail gracefully if any unforeseen exceptions are raised. This prevents counting outputs from being lost at the fault of the consistency checker. Consistency is checked after every run and is typically a very swift process (usually a fraction of a second). Nonetheless, a command line option has been added to tiny-count to allow this step to be turned off if needed. The following checks are performed for each library:

• Internal consistency for all assigned/unassigned read/sequence counts in alignment stats and summary stats
• Non-normalized Mapped Reads >= Normalized Mapped Reads
• Reported count totals in feature counts == reported count totals in rule counts
• Reported count totals in rule counts == assigned read count in summary stats (same for feature counts by transitive property)
• Reported count totals in rule counts <= its mapped reads row
• Reported counts per classifier have equal sums in feature counts and rule counts
• Total reads in mapped nt/len matrices == mapped reads in summary stats
• Total reads in assigned nt/len matrices == assigned reads in summary stats

Codebase Improvements

MergedStats classes have been mildly refactored to ensure that stats are complete and final before being validated and written to output files.

Closes #295

[taimontgomery]

Tested successfully with ram1 and Lib303 data.