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@AlexTate AlexTate released this 10 Mar 08:00
· 196 commits to master since this release
v1.3.0
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What's Changed

❗ = changes that present issues with backward compatibility

tiny-count

  • GFF files are no longer required, and if they aren't provided then sequence-based counting will be performed rather than feature-based counting. Stage 2 and 3 selection still takes place in this mode, and counts are still optionally subset by classifier. #279 #287
  • Shift parameters can be provided with overlap selectors. These parameters shift the 5' and/or 3' ends of matching feature intervals by the specified number of bases. #280
  • ❗ Anchored overlap selectors (all three) require that the non-anchored end of the alignment is nested within the feature's interval for a match #282
  • Wildcard values can be provided for overlap selectors. This is functionally equivalent to specifying partial. The full selector has also been renamed to nested. #282
  • A tutorial for tiny-count has been added. #272

tiny-plot

  • Class names in DGE scatter plots and class charts are sorted #286
  • Custom min and/or max view limits for DGE scatter plots can be specified in the Run Config #273
  • The "%" character has been removed from tick labels in class_charts and rule_charts #284
  • Various bugfixes and reliability improvements #273

Misc

  • Log files for workflow steps are placed in the logs subdirectory for reach run, regardless of the run's success/failure. This makes troubleshooting significantly easier. #276
  • A backward compatibility system has been introduced so that older Run Config files can be used if the user doesn't want to update them manually. The input file is left as-is but parameter additions/renames/deletions are automatically applied to the processed Run Config to bring it up to date. This is only supported for Run Configs from v1.2.0 and newer. #276
  • A new bowtie option -m has been added to the Run Config for specifying the drop threshold for reads with too many alignments #284
  • The ellipsis character, which Microsoft Excel autocorrects from three periods and saves using an obscure encoding format, no longer crashes the CSV reader. Empty rows are also skipped. #290
  • (tiny|tiny-count) --get-templates will avoid configuration conflicts by only copying files if none of the relevant filenames are present in the CWD. #272
  • The workflow runner shows longer descriptive argument flags in its output for tiny-* utilities #291
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