## FusionInspector v2.9.0
- upgraded Trinity to 2.15.1 along with minimap2 integration
- cleaner organization of outputs and IGV-inputs
- updated igv-reports with fusion ROI highlighting 
- misc updates for integration with ctat-LR-fusion

## FusionInspector v2.8.0 (Sept 30, 2022)
- compatible with :: delim fusion pairs - HUGO nomenclature
- revised cluster prediction to focus on cosmic-peak-enriched or artifact vs. other


## FusionInspector v2.7.0 (June 13, 2022)
- uses single pass mode instead of 2-pass to avoid potential input-dataset-specific effects on findings.
- use gene_id when gene_name not available
- still extract counter-evidence if single-end reads provided as input


## FusionInspector v2.6.0 (July 23, 2021)

uses STAR version 2.7.8a for compatibility with CTAT genome libs: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/
Incorporates predictions of fusions as COSMIC-like, artifact-like, or other based on sequence and expression characteristics. Use the new option --predict_cosmic_like
See https://github.com/FusionInspector/FusionInspector/wiki#evaluation-of-fusions-as-cosmic-like-or-likely-artifacts for details.


## FusionInspector v2.5.0 (Mar 1, 2021)
- incorporates microhomology analysis and plots for exploring likely artifacts
- duplicate removal more strictly handles duplicates and not excluding secondary alignments, important for certain alt fusion pairs ie. geneA--geneB but geneA--geneC is just as good.


## FusionInspector v2.4.0 (Jan 23, 2020)
- replaced picard dup marking w/ our own dup removal
- use tiedhash for storing read counts in get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl
- allow gzipped fusion lists
- set --chimSegmentReadGapMax 3 not --chimSegmentReadGapMax parameter 3
- get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl bugfix - only report unique results


## FusionInspector v2.3.2 (Oct 22, 2020)
- enabled use of multiple fastqs, set as comma-delimited list w/ input parameter

## FusionInspector v2.3.1 (Aug 10, 2020)
-minor bugfixes
-sync max intron len and max mate distance parameters w/ star-fusion
-improved support for single cell rna-seq processing

## FusionInspector v2.3.0 (Apr 7, 2020)
-compatibility updates for exploring IGH superlocus fusions (ie. w/ CRLF2)
-Pfam domains are shown in the interactive IGV-based FusionInspector html report view.
-incorporates EM for improved FFPM calculations and fusion fragment support assignment.
-can report isoform-specific evidence read fastqs


## FusionInspector v2.2.1 (Oct 18, 2019)
-reduce RAM consumption during spanning read analysis
-upgrade to STAR 2.7.2b
-upgrade igv-reports 0.9.6

## FusionInspector v2.2.0 (Sep 28, 2019)
-added --no_FFPM for applications where 'inspect' mode is used from STAR-Fusion and the FFPM values would be nonsensical.

## FusionInspector v2.1.0 (Aug 17, 2019)
-harmonized --output_dir usage w/ STAR-Fusion. Also, now accepting --STAR_max_mate_dist
-igv html file has fusion header info disabled for now. Will update later after igv callback mechanism in place for updates.


## FusionInspector v2.0.2 (Apr. 20, 2019)
-bugfix, avoiding over-counting split fragments now... if both frag reads overlap and provide split reads, we count the fragment once as intended now.
-upgrading STAR to 2.7.1a


## FusionInspector v2.0.1 (April 3, 2019)
-bugfix issue wrt submodule integration of fusion-reports
-updated docker to include use of STAR v2.7.0f


## FusionInspector v2.0.0 (Mar 20, 2019)
-uses annotation-based red-herring filtering as in STAR-Fusion for final report.
-restructured presentation of output files, final report called: finspector.FusionInspector.fusions.tsv
-self-contained stand-alone visualizations and reports using igv-reports
-docker support added


## FusionInspector v1.3.0 (May 1, 2018)
Simplified required arguments.  Using CTAT_GENOME_LIB env var for convenience.  Just needs fusion targets and reads and it'll run.
Capturing both pairs for the split-read fusion frags now for display in IGV.
Minor updates for py3 compatibility
FAF calculation is now FAR calculation (fusion allelic ratio instead of fusion allelic fraction ... documentation updated as to the difference).

## FusionInspector v1.2.0 (Feb 28)
Minor updates for compatibility with the latest STAR-Fusion and CTAT genome lib structure.


## v1.1.0 (July 24, 2017)
-Now mostly supporting FusionInspector as a submodule integrated into STAR-Fusion
-works with single-end as well as paired-end reads now.
-incorporates latest fusion-annotation and coding-effect analysis


## v1.0.1 (Feb 2, 2017)
include splice dinucleotides in report
stricter requirements for fusion evidence w/ NH and qual, and more sensible overlap definition for fusion-contrasting pairs
uses samtools v1.3


## FusionInspector Release v0.8.0 (July 28, 2016)
	-compute FFPM values correctly when using gzipped fastq files
	-upgraded SciedPiper and FusionFilter
	-updated FusionFilter better handles overlapping genes in the ref annotation
	-properly parse mismatch count from alignments and filter out lower quality alignments
	-mapping quality must be > 0 for fusion evidence reads
	-incorporated low seq complexity check for fusion evidence reads


## FusionInspector Release v0.5.0 (Mar 5, 2016)
Update to FusionFilter v0.1.0
removed unnecessary env vars, further cleanup, and documentation in sample data area.

## FusionInspector Release v0.4.2 (Feb 2016)
Wiki documentation is updated, removed environmental variable requirements that were unnecessary, and added a README.txt

## FusionInspector v0.4.1 (Jan 6, 2016)
bugfix - fusion spanning and junction read evidence bam files once again written correctly.

## FusionInspector v0.4.0 (Dec 16, 2015)
Includes FFPM (fusion fragments per million total rna-seq reads) normalized evidence support measurements in the summary output.

Runtimes w/ STAR are now much faster and slightly more sensitive while retaining low false positive rates. Be sure to use the very latest STAR software.


## FusionInspector v0.3.3 (Nov 19, 2015)
includes filtering of repetitive reads

## FusionInspector v0.3.2 (Nov 12, 2015)
Uses the very latest STAR software, outputs only those alignments corresponding to the fusion contigs.

## FusionInspector v0.3.1 (Nov 8, 2015)
no longer using kmer read filter when leveraging STAR, as it's unnecessary and just adds to runtime and resource requirements.

## FusionInspector v0.3.0 (Nov 2, 2015)
Initial release. See wiki for documentation.

## FusionInspector Pre-Release v0.2.0 (Aug 10, 2015)
Filters out repetitive reads based on kmer composition.

Ensures that the spanning support frags are each entirely mapped separately to the different genes (not involving junction reads) and are actually concordant (not relying on the bit flags that aren't always set according to expectations).

## FusionInspector v0.1.0 Pre-Release (July 21, 2015)
slimmed down for faster execution, making IGV-prep an option rather than mandatory.

## FusionInspector pre-release v0.0.1 (July 9, 2015)
First pre-release
