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

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

Version 1.0.6

Stable version with IR operations and quadripartite genome structure being optional

Version 1.0.1

v1.0.1

Update to version 1.0.1