CHANGELOG.md

CHANGELOG

Version 1.1.3 (2024.05.31)

• Refactoring of coverage to an R6 class
• Updates to how outliers are handled for artifacts created by scripts_for_figures_tables

Version 1.1.2 (2024.05.25)

• Updates to summary tabular statistics files
  • Inclusion of unpartitioned statistics for coding and noncoding regions summaries
  • Standardize name of summary groups to Chromosome
  • Update WRSD metric to in terms of kilobases
• Updates to scripts_for_figures_tables
  • Figure1 updated to use manual jittering for boxplot with outlier labels
  • Include Figure1b in output file
  • Changes to value exactness in some tables

Version 1.1.1 (2024.05.21)

• Minor fixes to tabular statistics file creation
• A coverage of 0 for a window is always labeled as low coverage

Version 1.0.10 (2024.03.23)

• Dynamic changes to IRCheck as PACVr.complete() progresses
  • If no samples from gbkFile contain the qualifiers needed for specified analysis, continues with IRCheck = NA
  • If no IR regions are identified, continues with IRCheck = NA
  • If there are missing IR regions needed for synteny test, continues with IRCheck = 0
  • If no synteny is found, continues with IRCheck = 0
  • When tabularCovStats = TRUE, if IR mismatches are identified, continues with IRCheck = NA
• For tabularCovStats = TRUE, summary data corresponding to the complete genome is included in <sampleName>_summary.regions
  • <sampleName>_coverage.summary.regions has been renamed <sampleName>_summary.regions
  • The number of ambiguous nucleotides is always counted, named N_count
  • When synteny testing is indicated by IRCheck and possible, as detailed above, the number of mismatches between the IRs is counted as IR_mismatches
• The evenness metric for tabularCovStats has been renamed E_score

Version 1.0.9 (2024.03.01)

• Improving variable and file names
• Correcting output plot specifications
• Increase logger use, improve logger format

Version 1.0.8 (2024.02.28)

• Handling of GenBank features with multiple qualifiers of the same name
• Coverage summaries added to verbose output files
• Parameters syntenyLineType and regionsCheck for PACVr.complete() have been combined into IRCheck
• Support for PNG output
• Samples without note can be used for standard coverage analysis
• Sample name in BAM file can match either VERSION or ACCESSION of GenBank file for verbose analysis
• Analysis continues without regions when IR presence test unsuccessful

Version 1.0.7 (2024.02.01)

• More robust parsing of feature sequence locations using INSDC standards
• Exception handling for attempted reading of GenBank data
• "Repair" GenBank data with unqualified features to handle read.gb bug
• Preemptively checks for presence of data property necessary for specified analysis, with logger info in case of issues

Version 1.0.6 (2024.01.07)

• Moved functions reg. IRs, quadripartite structure into separate file
• Made various plastid-specific functions optional

Version 1.0.5 (2023.12.07)

• Minor bugfixes
• New version submitted to CRAN

Version 1.0.4 (2023.12.06)

• Implemented a logger
• Several bug fixes (e.g., error caused by function masking)
• Resolve warning caused by depreciated 'dplyr' use
• Resolve need for library calls to RCircos within the code

Version 1.0.3 (2023.10.05)

• Replacing dependency 'genbankr' with 'read.gb' and custom functions
• Addition of new contributor: Gregory Smith

Version 1.0.2 (2023.10.04)

• Cleaning up of code

Version 1.0.1 (2021.04.30)

• Merging changes by Nils Jenke into master

Version 1.0.0 (2021.04.16)

• Updates to allow new analyses

Version 0.9.5 (2020.11.18)

• Minor updates to keep PACVr compatible with CRAN

Version 0.9.4 (2020.09.18)

• Updated README file
• Updated PACVr_Rscript.R
• Updated PACVr-complete.Rd file
• Updated PACVr_Vignette.Rnw
• Replaced flag delete with verbose
• Added additional output regarding the quality of the assembly

Version 0.9.3 (2020.07.27)

• Updated README file
• Updated DESCRIPTION file
• Updated PACVr-complete.Rd file
• Updated PACVr-package.rd file
• Updated package vignette
• Updated Unix command-line shell script of PACVr
• Removed system requirement mosdepth
• Added Windows compatibility
• Added low coverage output

Version 0.9.2 (2020.02.10)

• Updated README file
• Updated and improved package vignette
• Updated Unix command-line shell script of PACVr

Version 0.9.1 (2020.02.07)

• Updated README file
• Updated and improved package vignette

Version 0.9.0 (2020.01.31)

• Added functions that add tick marks and position information (in kb) in regular intervals to the genome visualization
• Added functions that evaluate sequence equality among inverted repeats and, if detected, provide reports on differences
• Added functions that enable users to specify the threshold value below which histogram bars are displayed in red as relative value
• Improved the scaling of various vector elements (e.g., fonts) for visualizations of unusually small (<100kb) or unusually large (>200kb) plastid genomes

Version 0.8.2 (2019.09.12)

• Several minor bug fixes

Version 0.8.0 (2019.07.09)

• Several minor changes to make package compatible with CRAN

Version 0.7.5 (2019.07.05)

• Several minor changes to make package compatible with CRAN
• Several minor improvements to DESCRIPTION and NAMESPACE
• Bug fix to import RCircos.Env

Version 0.7.0 (2019.07.03)

• Several minor bug fixes

Version 0.6.0 (2019.06.14)

• Several minor code improvements
• Several minor improvements to DESCRIPTION and NAMESPACE

Version 0.5.0 (2019.06.13)

• Several minor improvements to DESCRIPTION and NAMESPACE
• Several minor improvements to manual and vignette

Version 0.4.0 (2019.06.12)

• Several minor code improvements
• Several minor improvements to DESCRIPTION and NAMESPACE
• Added example data (inst/extdata)

Version 0.3.0 (2019.05.24)

• Several minor code improvements
• Added preliminary manual
• Added preliminary vignette

Version 0.2.0 (2019.03.15)

• Added function PACVr.complete
• Added function SplitCovAtRegionBorders in calcCoverage.R
• Added preliminary documentation files.