# ctat-LR-fusion v1.0.0 Oct 8, 2024
- works well for both ONT and PacBio under default params.
- excludes alignment overlaps between gene pairs that fall within sequence-similar regions, and requires at least 25 bases (default) of exon overlap in the remaining regions.
- excluding neighbor-overlap gene pairings and additional annotation-based filtering between phase-1 and phase-2.
- added --FI_extra_params custom parameter to pass through STAR parameters to F
- included option for --examine_coding_effect



# ctat-LR-fusion v0.13.0 Jan 27, 2024
- allow for paralog alignments to be included
- pursue additional candidates where one breakpoint is initially <= MAX_EXON_DELTA and the other is within 1kb and there's multiple reads suggesting it.
- with multiple reads suggesting fusion, use the min value for the deltas in phase 1 for candidate selection.
- reorganization of preliminary candidate intermediate output formatting for easier tracking and troubleshooting of findings.
- igv-reports v1.11.0 which has default ordering of fusions according to descending read support in the html.



# ctat-LR-fusion v0.12.0 Jan 02, 2024
-  igv html working with long and short reads together
-  results sorted by descending countws of supporting reads
- in combined long/short mode, retain any fusion calls with illumina reads that meet the min read requirements regardless of dominant isoform fraction results
- added option  --chim_candidates_only to just get the initial list of chimeric candidate



# ctat-LR-fusion v0.11.0 Oct 12, 2023
- leaner on disk space usage by sam->bam streamed
- include igv files bundle as output
- adding LeftGene and RightGene info thats retained on short read integration
- allow secondary alignments in phase 2 (important for retaining read support abundance across paralogs)


# ctat-LR-fusion v0.10.0  Aug 19, 2023
- more optimization of ctat-minimap2
- bugfix to ROI definition off-by-one on acceptor site for igv-report display
- include LeftGene and RightGene columns
- added get_MAS-seq_fusion_cell_barcoding.py for supporting sc-MAS-seq analysis (single cells and long reads)

# ctat-LR-fusion v0.9.0
- ctat-minimap2 update for chimeric reads 
- includes default filtering at the 0.1 FFPM threshold
- igv-reports upgrade, better performance and highlight fusion breakpoints as ROIs

devel versions:
      # --discarded-- (ctat-LR-fusion v0.8.0  
      - incorporates latest ctat-minimap2 with additional alignment filtering during chimeric mode for phase-1 of ctat-LR-fusion finding.
      - (performance issues, do not use)

      # ctat-LR-fusion v0.7.0
      - included --min_FFPM (with default at 0.1), important when tackling massive data sets to avoid pursuing hundereds of thousands of candidates in phase 2.


# ctat-LR-fusion v0.6.0
- bugfixes for non-ref-splice coordinate assignments
- added option: --snap_dist <int>               :  if breakpoint is at most this distance from a reference exon boundary, position gets snapped to the splice site.
- added option: --min_frac_dom_iso_expr <float>     : minimum expression of dominant isoform (default: 0.05)
- adjusted minimap2 alignment params used.
- exits gracefully if no fusions found in initial phase.
- cleaner organization of IGV-prep files.


