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@AlexTate AlexTate released this 03 May 05:38
· 104 commits to master since this release
v1.4.0
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Learn about vigilant mode.

What's Changed

tiny-count

  • A new selector has been added to the Features Sheet to allow for selecting reads based on their edit distance to the reference. It is evaluated during Stage 2 selection. #298
  • BAM files are a supported input filetype. SAM and BAM file headers are checked during each run to ensure they report compatible ordering. Additionally, the Samples Sheet is more rigorously validated during standalone runs. #304
  • Normalization by genomic hits can be disabled, independently or in tandem with normalization by feature hits. Regardless, the collected stats are validated for internal consistency after all samples have been counted. #301
  • When using diagnostic options, intermediate alignment tables are written in CSV format and include new useful information #300

tiny-plot

  • Features are included in DGE scatter plots if they have a count of 0 in one of the two conditions being compared. They are shown at the very edge of the plot space as half circles. Previously they were omitted due to the log scale's singularity at 0. Features that have a count of 0 in both conditions are still omitted. In DGE class scatter plots, classes consisting entirely of 0 counts in both conditions are still omitted from the legend. #305

Misc.

  • Some Run Config options have been removed due to redundancy and deprecation: Bowtie's trim5 and trim3 options, and tiny-count's counter_all_features option #305

Full Changelog: v1.3.0...v1.4.0

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