Changes since last release v2.0.0
Major changes:
- Updated the input parameters of Bambu to simplify the user experience
- Introduced NDR threshold recommendation
- Implemented trainBambu(), allowing users to train and use models on their own data
- Reads that cannot be assigned to any transcript are grouped as incompatible counts
- Partial estimates are removed from output as it can be directly obtained based on total count estimates and full-length count estimates
- The fusion mode is now available, which assigns read classes that align to multiple genes to a new combined fusion gene
Minor changes:
- Novel transcripts and genes are now by default output with a Bambu prefix
- Updated the documentation, messages and errors output by Bambu
- Annotated transcripts (with unique exon-junctions) with at least 1 full-length read are assigned a NDR rank
- Fixes crash during Low Memory Mode when there are scaffolds with no reads
- Fixes crash on windows machines caused by DNAStringSet
- Adds NDR metadata when running discovery mode with recommended NDR, so users do not need to look at console for the recommended NDR.
- Re-enabled GitHub actions for new devel branch name and the windows check
- Fixed a crash that occurs with large datasets resulting in large overflow tables during novel gene id assignment
- Remove nested bplapply in EM
- Remove unused eqClassById list column in the readClassDist object to reduce memory usage
- Fixed a bug that caused identical unspliced reads to not be tracked when trackReads = TRUE