Jonathan Göke

- add a unit test for `writeBambuOutput()`

implement post filter function based on average across all samples

1

- currently implemented in fusion gene mode for just the subset filter - Additional filters could be added - documentation is needed

estimate relative read count/ subset read count for final annotation object

1

- estimate the relative read count for each transcripts based on the sum of all reads across all samples - estimate the relative subset read count (based on read counts...

replace assignGeneIDexonMatch with assignGeneIDs

1

- use a single function for this task (assignGeneIDs ranks by similarity) - make consistent how transcripts are assigned that match genes through intermediate novel transcripts: assign read class to...

enable fusion transcript discovery with bambu

1

Include a fusion transcript discovery and qantification mode: - input requires reads that are aligned to a "fusion genome" that includes the predicted breakpoints" - input requires the "fusion genome"...

estimate promoter activity from bam file

2

Implement an option to estimate promoter activity from bam files (currently proActiv requires the junction files from TopHat2 or STAR)