# SeqKat 0.0.9
===========================
- Updated email for pboutros to @sbpdiscovery.org
- Changed GitHub organization reference from uclahs-cds to theboutroslab

# SeqKat 0.0.8
===========================
- Updated email for pboutros
- sorting out CRAN checking issues with 0.0.7
- fixed a typecast issue for systems where int is not compatible with size_t

# SeqKat 0.0.7
===========================
- Removed the flags that strip cpp debug headers

# SeqKat 0.0.6
===========================
- Removed 'SeqKat' in single quotes from the Title field of the DESCRIPTION file as requested by CRAN maintainer
- Removed 'SeqKat' in single quotes from the start of the Description field of DESCRIPTION file as requested by CRAN maintainer
- Added DOI to Description field of DESCRIPTION file as requested by CRAN maintainer
- Added 'SeqKat' in single quotes Title and Description field of DESCRIPTION file as requested by CRAN maintainer
- Modified the seqkat() function to not setwd() into the output.dir set by the user since you aren't allowed to chdir to /tmp on CRAN test servers
- Switched "." in tests to tempdir() to avoid writing in the homedir of CRAN test servers
- Wrote runnable tests to replace the \dontrun{} tests and added RData files based on the bed file in the test directory for the intermediate functions to be tested with

# SeqKat 0.0.5
===========================
- Added knitr to the Suggests and VignetteBuilder fields of the DESCRIPTION, causing changes to the vignette index which CRAN requires
- Fixes for the Makevars file to support Solaris, as well as minor changes to the lookup symbols for the C++ functions due to changes in R 3.4.3
- Added proper array size to char array to fix memory leak
- Switching from rmarkdown to knitr for rendering the vignette


# SeqKat 0.0.4
===========================
- Figured out which c++ flags are required to strip out unnecessary headers from the object files
- Adding the correct vignette builder to the description, fixing docs and removing a bed file from the old location
- Vignette fixes
- Updating the docs with the new example from roxygen
- Added an example dataset


# SeqKat 0.0.3
===========================
- Allocating and deallocating the trinuc array properly
- Adjusting how we instantiate Rcpp::NumericVector's since windows is bad at overloading Rcpp functions apparently
- Moving doMC to the suggests section
- Changed maintainer and added doParallel
- Updated description and authors
- Added Roxygen2 docs
- Added chromosome length file for GRCh38
- Added generate.trinucleotide.counts, a script to make the tn counts file


# SeqKat 0.0.2
===========================
- Improved the docs/vignette
- Added the get.trinucleotide.counts function to allow the user to generate their own count file (which supports hg38 now)
- Added lots of error handling and refactored to allow for individual chrs and/or bed files to be handled (so HPCI can handle the parallelization better)


# SeqKat 0.0.1
===========================
- Modified to allow the user to provide a file containing the lengths of the chromosomes for their desired reference, with a default file for hg19 stored in extdata
- Fixing a bug where chromosomes with few SNVs try to write a list of lists to an output table
- Added error handling and examples
- Added documentation for the new main seqkat function, and added params for the ref.dir and bed.dir
- Full restructure of SeqKat into a standard Rcpp package, with two extdata files (tn_count.txt and length_hg19_chr.txt)

