Version 1.1.3

• 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

• 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

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

Version 1.0.11

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

Version 1.0.10

• 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

Version 1.0.9

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

Version 1.0.8

• 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

• 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