TALON v6.0

Readthrough transcription detection and gene assignment improvement

• Added option to base talon, --create_novel_spliced_genes, which will create a novel gene if a spliced read is found that does not share splice junctions with any genes, but does overlap an existing locus or loci in the reference
• Improved gene assignment for novel transcripts
  - Reads that contain splice sites that overlap splice sites in a set of multiple non-overlapping genes (without shared
  splice sites) are assigned to novel genes with the novelty label fusion
  - Reads that contain splice sites that are shared between a set of multiple genes (ie the genes overlap) are now tiebroken
  based on distance of read's 5' / 3' ends to transcripts from this gene set
  - This change improves performance on annotating reads and transcripts to the right gene and thus improves gene
  quantification as well

Single-cell support

• Added option to talon to use cell barcodes in the alignment files as separate datasets (--cb)
• Added utility to output TALON quantifications in AnnData format (talon_create_adata). Particularly useful for single-cell and large datasets where dense matrix representation is prohibitive. Capable of generating both gene- and transcript-level AnnDatas

Requirements changes

• Removed pybedtools as a requirement as it was breaking installs and is not required
• Restriction of Python versions to <=3.6 and >3.8, as Python 3.8 changes the behavior of variable sharing across multiprocessing threads (https://stackoverflow.com/questions/70552775/multiprocess-inherently-shared-memory-in-no-longer-working-on-python-3-10-comin)

Miscellaneous

• Added option to talon_filter_transcripts to exclude ISM transcripts (--excludeISMs)
• Added option to talon_filter_transcripts to include all transcripts from the reference annotation, regardless of whether they were observed in the datasets or not (--includeAnnot)
• Added script to return the longest observed ends for each transcript instead of the ones reported by TALON (call_longest_ends)
• Added --verbosity option to talon to tune how much output the user sees (0 = only errors, 1 = logging, 2 = debug)
• Added support for BAM files as input in addition to SAM files
• Added multithreading to SAM to BAM compression
• Fixed minor bugs with temporary output directory behavior