Implemented makeDF which uses Rsamtools to read the coverage data directly from the BAM files (per chr), applies the cutoff just like in makeDb, and creates a DataFrame with the data of interest. Tweaked a lot of functions in order to pass R CMD check (technically there is 1 warning left, but that is because the license has yet to be specified). Some of the examples like in getAnnotation, supportedTables had problems and were moved into dontrun calls. Package dependencies were updated and sqldf was slighly modified because the package RpgSQL is no longer in CRAN. All require statements now use quotes in order to pass R CMD check.
Merged the changes in getLimmaInput with Alyssa's mid-May modifications
Updated the documentation in getF.R to pass R CMD check via check() from devtools, and also check_doc()
Modified makeDF so it will include the position index. Implemented getLimmaInput using the results from makeDF into the function getLimmaInput.DF. Modified getLimmaInput's 'gathering results' section by using lapply's instead of incrementally generating the results.
Version bumped to 1.0.2. Introduced get.pvals.DF and with this function the whole pipeline using Rsamtools/IRanges should be complete
Minor modifications so that IRanges is imported. Testing getLimmaInput.DF
Fixed a small bug in getLimmaInput.DF
Merge pull request #3 from lcolladotor/master

Version 1.0.2 of derfinder.