Release Notes 2.0.2

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Note: If you are a RUM 1.x user and you haven't read the release notes for RUM 2.0.1, please do so. That version contains lots of changes from RUM 1.x.

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RUM 2.0.2 contains some minor fixes on top of 2.0.1.

Fix accuracy issue in mapping_stats.txt file

In 2.0.1, the "number of bases covered" counts in the mapping_stats.txt file were incorrect, and they were often well over 100%. This has been fixed in 2.0.2.

Add RUM job report file

As of 2.0.2, you will find a file called rum_job_report.txt in the output directory when you run a job. This file contains a listing of the parameters that were used to run the job, and the timestamp of some major milestones: when preprocessing started and finished, when each chunk finished, and when postprocessing finished.

Fix a couple regressions in output files

In 2.0.1, we had a regression where the novel exon quantification file (novel_inferred_internal_exons_quantifications...) incorrectly contained the gene-level quantifications, and not exon quantifications. This is fixed in 2.0.2.

The header row was missing from the junctions_* files.

Improvements to documentation and warning messages

The documentation for a few options has been expanded in the output of rum_runner help and rum_runner help align. Some of error messages that you'll get if you enter invalid options have also been clarified.

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The full list of issues addressed in this release is here.