bambu v3.2.0 (change date: 2023-Apr-26)
==========================================
Minor fixes:
    * 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

bambu v3.0.8 (change date: 2023-02-14)
==========================================
Minor fixes:
    * Bug fix for writeOutput function to remove unused argument due to dplyr package update
    * Correct CPM calculation to incorporate incompatible reads 
    * Round up quantification estimates to 5 digits (customisable through opt.em argument) 


bambu v3.0.0 (Change date: 2022-10-25)
===========================================
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 and used to calculate more accurate gene expression estimates
    * The fusion mode is now available, which assigns read classes that align to multiple genes to a new combined fusion gene
    * Improved quantification processing time by reorganising quantification steps 

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
    * Partial estimates are removed from output as it can be directly obtained based on total count estimates and full-length count estimates

bambu v2.2.0 (Change date: 2022-04-27)
===========================================
Major changes: 
    * Implemented a de-novo mode where no annotation is provided
    * Implemented trackReads to allow users to track read to transcript model map
    * Implemented outputDistTable to output the distance metrics bedtween read class and transcript models
    * Allow input files without specific extension for fasta and annotation gtf files (gff etc)
    

Minor fixes:
    * Fix the bug when reads are aligned outside the supplied genome and 
    * Provides a warning and issues with bsgenome and their strand.
    * Provides a more informative error when running in denovo mode if no transcripts pass the threshold
    * Fix bug in runs where annotation gene names had "gene" 

bambu v2.0.4 (Change date: 2022-02-08)
===========================================
Minor fixes: 
    * Fix out of bounds aligned reads bug
    * Fix bsgenome strand bug
    * Make error clear when in the de novo mode and threshold is too low
    * Move NDR out of discovery parameters list
    

bambu v2.0.3 (Change date: 2022-01-30)
===========================================
Minor fixes: 
    * Skip the errors when txScore is not calculated

bambu v2.0.1 (Change date: 2022-11-23)
===========================================
Minor fixes: 
    * Update saved objects using updated Bioc 3.14 packages 

bambu v2.0.0 (Change date: 2021-10-18)
=============
Major Changes:
    * Implemented a machine learning model to estimate transcript-level novel discovery rate
    * Implemented full length estimates, partial length estimates and unique read counts in final output
    * Improved the performance for the extend-annotations module with simplified code
    * Improved the performance when large amounts of annotations are missing.
    * Implemented a lowMemory option to reduce the memory requirements for very large samples (>100 million reads)

Minor fixes:
    * Remove the use of get() which looks into environment variables (prone to crashes if a variable of the same name exists) and directly references the functions that should be used instead. 
    * Fixed the error when a .fa file is provided as a string variable in non-windows system
    * Fixed the error when no single exon read class is provided in any samples
    * Fixed the bug when no splice overlap is found between read classes and annotations

bambu v1.0.2 (Change date: 2020-11-10)
==============

Changes:
    * Bug fix for author name display
    * Bug fix for calling fasta file and bam file from ExperimentHub
    * Update NEWS file 

bambu v1.0.1 (Change date: 2020-11-06)
==============

Changes:
    * Bug fix for parallel computation to avoid bplapply

bambu v0.99.4 (Release date: 2020-08-18)
==============

Changes:
    * Remove codes using seqlevelStyle to allow customized annotation
    * update the requirement of R version and ExperimentHub version



bambu v0.99.1 (Release date: 2020-08-18)
==============

    * First submission to BioConductor
