Andre Sim

DO NOT MERGE - This PR is just for review purposes to make it easier to isolate the NDR changes in the BambuManuScriptRevision branch. This pull request involves several features...

Remove rcfiles input parameter, Now users can use reads with either a vector of .bam paths, a vector of .rds paths, or a list of rcfiles (must be RangedSummarizedExperiment, such...

Don't compress gene assignments before fusion assignment

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Fixes issue where fusion mode didn't work with the new geneID assignment function Issue was that genes were compressed before fusion mode had a chance to analyse them

Add lowConfidence transcripts to output and improve NDR filtering options

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- In this PR transcripts that are normally filtered out including subset transcripts and those above the NDR threshold are placed into the metadata of the annotations in $subsetTranscripts and...

**Work in progress. Do not use or run** In this PR transcripts that are normally filtered out including subset transcripts and those above the NDR threshold are placed into the...