NEWS

TrIdent 3.21

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

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.

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

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.

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

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

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.

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

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)'

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