## Changes in 1.5.2

+ Add option to use local or global DIRECT search with `globalLocal` parameter. 
The default is local.
+ Add `geneSearch` function! This new function allows users to search
for genes or gene annotations of interest on positively classified contigs using 
a gff file imported into R with the Bioc.gff package.

## Changes in 1.5.1

+ Implement DIRECT search algorithm during pattern-matching. Major speed 
increases with minor changes to resulting classifications. Use DIRECT by setting
`searchMethod`="direct". For now, the original "grid" search method remains the
default. 
+ Minor bug fixes and documentation updates

## Changes in 1.3.2

+ Make the minimum sloping pattern widths a variable in TrIdentClassifier() 
('minSlopeSize').
+ Fixed minor bug where contigs smaller than a minimum pattern width would 
still allow one pattern variation to be tested.

## Changes in 1.3.1

+ Make the median VLP:WC minimum ratio for HighCovNoPattern classifications a 
variable in TrIdentClassifier() ('minHCNPRatio').

## Changes in 1.1.5

+ Added names to list items in pattern matching results.
+ Fixed bug that caused an error when there were no "Prophage-like", "Sloping"  
and "HighCovNoPattern" classifications made.
+ Added verbose for when there are no "Prophage-like", "Sloping" 
and "HighCovNoPattern" classifications made.
+ Cleaned specializedTransductionID() output table. 

## Changes in 1.1.4

+ Fixed bug caused by using the 'specificContig' parameter in the 
specializedTransductionID function.

## Changes in 1.1.3

+ Added ability to normalize VLP-fraction:whole-community read coverage ratio
by the number of reads in both the VLP-fraction and whole-community. 

## Changes in 1.1.2 

+ Fixed bug where an error was caused when calculating a ratio with contigs in 
which the median whole-community non-prophage-like read coverage value was 0.
+ Added 'onlyPlot' parameter in plotTrIdentResults() function.
+ Added 'logScale' option in plotTrIdentResults() function.
+ Removed 'suggested filtering threshold' feature.

## Changes in 1.1.1

+ Fixed bug where an error was caused when calculating VLP:WC read coverage 
ratio with contigs in which the median whole-community read coverage value was 
0.

## Official release of TrIdent V1 on Bioconductor 3.21!

## Changes in 0.99.3

+ Updated vignette to print a select few plots rather than all the output 
plots
+ Added a text document to the inst/script/ directory with specific code and 
instructions for generating the sample pileup files used in the examples, vignette
and README
+ Fixed bug with verbose argument where verbose=FALSE still printed messages to 
the console
+ Updated use of 'if(verbose == TRUE)' to 'if(verbose)'

## Changes in 0.99.2

+ Updated vignette and README with BiocManager installation instructions
+ Moved Acknowledgements, Funding, and SessionInfo() to 'supplemental 
information'
section in vignette
+ Changed TOC_depth from 2 to 3 in vignette
+ Updated formatting of NEWS file
+ Grouped related functions in .R files for easier troubleshooting
+ Add verbose = TRUE/FALSE argument to allow users to choose whether to print 
progress
+ Added co-authors to DESCRIPTION file
+ Added additional logic for input file validation
+ Added better descriptions of input file requirements in the main function 
.man pages
+ Added rendered summary histogram plot to output list 
+ Removed all usage of <<-
+ Fixed improper usage of lapply

## Changes in 0.99.1

+ Fixed unit tests for Bioc submission

## Changes in 0.99.0

+ Bioc submission
