Bug fixes

(#51) Fixed a filtering bug that wrongly flagged as ineligible cases where proportion shifted 100% from one isoform to another (meaning 0 reads in all other isoforms). Although critical in theory, our trials showed negligible impact in practice, as even a single read on another isoform would negate this bug.
(#49) Results obtained from inconsistent annotation usage used to be explicitly left with NA values, but this caused plotting functions to fail. RATs will now handle this better. Inconsistencies are caught at the beginning of the run. If execution is forced despite them, RATs will replace NA counts with 0 at the end of the run, to allow plotting of genes with a mixture of consistent and problematic isoforms. Proceeding with annotation inconsistencies remains a scenario strongly advised against.

Enhancements

(#48) The noise threshold is now additionally applied to the gene as a whole in each condition, not just to individual transcripts. The idea is to enable preventing gene switch-on/off events from getting picked up as DTU due to the artificially massive proportion shifts caused by low counts in one of the conditions.
(#52) Annotation inconsistencies are no longer silently ignored. Transcript IDs are now checked more thoroughly for consistency across samples and between samples and annotation. Now RATs will abort the run if the sets of IDs differ in any way. Execution can be forced using the reckless parameter, if necessary and if justifiable by circumstances, but as the name suggests this is dangerous territory. Mixing annotations remains a very bad idea.