---
* The -q --qvalue option now works by including splice junctions within the specified range. To
preserve the previous behavior, use -q 0.01 1. The default -q 0 1 disables filtering.
* The -c --canonical argument now defaults to False. To preserve prior behaviors, manually set the
-c flag to translate canonical proteins detected in the RNA-seq experiments even if isoform translation failes
* The -c --canonical argument now will translate a canonical sequence even if a splice event has low skipped
junction counts or falls outside of the specified fdr range
* JCAST now automatically models the likely translatable junction count threshold through the -m --model argument.
Previously this was done manually then set as an integer (minimal read count) using the -r --read argument.
* The skipped junction counts used for modeling now consider the sum of all biological and technical replicates
rather than the minimum