# AssessORF 1.7 Changes in version 1.7.1 (2020-10-23) * Genome viewer plots will now show the forward strand above the reverse strand, and reading frames will now be laid out in 1 through 6 order moving down the genome viewer (before it was reversed) Changes in version 1.7.0 (2020-10-21) * Can now toggle interactivity of the genome viewer when plotting Assessment objects * Can now zoom into an initial range with the genome viewer when plotting Assessment objects * Documented the genome viewer in the plot.Assessment man page * Added a genome viewer example to the vignette * Fixed a bug that was causing an error when users attempted to zoom out ten-fold with the genome viewer plot # AssessORF 1.3 Changes in version 1.3.1 (2019-10-22) * Data for six new strains, S. pyogenes AP1, E. coli BW25113, S. aureus HG001, L. lactis MG1363, B. subtilis NCIB 3610, and L. monocytogenes 10403S, have been added to AssessORFData * CITATION file added as corresponding paper has now been published * Updated MapAssessmentData such that verbose output is cleaner and more informative # AssessORF 1.1 Changes in version 1.1.7 (2019-04-29) * Added a function, CompareAssessmentResults, for comparing two results objects against each other * Added a processors parameter to MapAssessmentData for compatibility with DECIPHER functions Changes in version 1.1.6 (2019-04-07) * Added parameters to AssessGenes to bound the range in which to look for conserved starts that can serve as alternative options to a predicted start * Added a parameter to AssessGenes that requires ORFs with protein evidence but no predicted start to have a certain minimum number of peptide hits in order to be included in the final output Changes in version 1.1.5 (2019-01-11) * Update to how conserved starts and conserved stops are utilized in AssessGenes * Removed weighted score * Made clarifications to the man pages * Minor edits to the vignette Changes in version 1.1.4 (2018-12-15) * Updated AssessGenes to make sure predicted stops are valid for their corresponding genes, and users will be warned appropriately if a predicted stop is invalid * Minor updates to plots * Bug fixes on previous version's MapAssessmentData updates Changes in version 1.1.3 (2018-11-12) * Fixed a bug affecting coverage related to gaps in alignments in MapAssessmentData * Used exponential moving averages to filter out bad alignment regions in MapAssessmentData Changes in version 1.1.2 * Implemented a fix to the vignette so it builds without an internet connection Changes in version 1.1.1 * Reduced time it takes to run MapAssessmentData examples # AssessORF 0.99 Changes in version 0.99.22 * Added data package to Suggests list * Tweaked connection to data package in the AssessGenes function Changes in version 0.99.21 * Minor edits to man pages and the vignette Changes in version 0.99.20 * Minor edits to man pages and the vignette Changes in version 0.99.19 * NEWS file added