[ ] Please rename any variable and function called "verbose" or "verboseInformation()" with "printCovStats()" (or words to that effect), which is a more factual description.
[ ] Please rename function called "writeTables()" with "printCovValsAsTable()" (or words to that effect), which is a more factual description.
Extension/Revision of function writeTables()
[ ] It would be fantastic if the coverage statistics saved via writeTables() could be calculated irrespective of the value of analysisSpecs$isIRCheck. After all, the IRCheck only has a relevance for step 3 of verboseInformation() in helpers.R, where writeTables() in its current implementation expects the exact location information of the IRs. What is needed is a second, simpler version of writeTables() that does not operate on the four regions of a quadripartite genome but simply on the entire undivided genome. This simpler version is simply executed when IRCheck=False.
Renaming
Extension/Revision of function writeTables()
writeTables()could be calculated irrespective of the value ofanalysisSpecs$isIRCheck. After all, theIRCheckonly has a relevance for step 3 ofverboseInformation()inhelpers.R, wherewriteTables()in its current implementation expects the exact location information of the IRs. What is needed is a second, simpler version ofwriteTables()that does not operate on the four regions of a quadripartite genome but simply on the entire undivided genome. This simpler version is simply executed when IRCheck=False.