STAR-Fusion Release v1.3.1

	This is a major update and includes the following changes:

	-overall structure of intermediate outputs makes it more straightforward to follow the fusion evidence and fusion prediction filtering and troubleshooting (to be well described in updated documentation soon).

	-the human fusion annotation database was expanded to include some new resources, all described here:
	https://github.com/FusionAnnotator/CTAT_HumanFusionLib/wiki

	-the 'red herring' category of fusions (see above wiki) are now by default auto-filtered from the final output. You can turn off annotation-based filtering with: STAR-Fusion --no_annotation_filter

	-fusions are automatically filtered out based on minimum fusion evidence requirements set based on the number of input reads. A minimum of 0.1 fusion fragments per million total fragments (FFPM) are required as a default (set with: STAR-Fusion --min_FFPM)


STAR-Fusion Release v1.2.0
	Added --bbmerge : runs STAR w/ paired-end reads but then also runs STAR using 'super-reads' assembled via the bbmerge software.  This helps in cases where fragments are short and/or the paired-end reads overlap.
	Bugfixes related to inframe vs. frameshift detection wrt setting coding phases of exons.
	Removed filtering of blast-pairs where sequences are shared due to physical overlap on the genome (false negatives).
	FusionInspector 'inspect' and 'validate' modes write to corresponding separately named directories.
	Plug-n-play ctat genome libs are updated wrt removing blast pairs for overlapping genes and CDS phasing information for reference proteins. (GRCh37_gencode_v19_CTAT_lib_Nov012017 and GRCh38_gencode_v26_CTAT_lib_Nov012017)
	Including new CTAT genome lib for Mouse v. M15 to support mouse cancer studies.

	Instead of downloading the new ctat genome lib, users can patch the earlier: GRCh37_gencode_v19_CTAT_lib_July192017 or GRCh38_gencode_v26_CTAT_lib_July192017 involving 3 steps:
	   cd /path/to/existing/ctat_genome_lib_dir
           STAR-Fusion/FusionFilter/util/index_blast_pairs.remove_overlapping_genes.pl .
	   STAR-Fusion/FusionFilter/util/build_prot_info_db.pl --gtf ref_annot.gtf --genome_fa ref_genome.fa --out_prefix ref_annot

	
STAR-Fusion Release v1.1.0
	Much new functionality is included in this release v1.1.0:
	Note: v1.1.0 requires a new CTAT_genome_lib: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/
	annotating fusions based on known cancer fusions (--annotate)
	exploring the effects on fused coding regions, reconstructing candidate fusion transcripts and fusion proteins (--examine_coding_effect)
	extracting the fastq reads that provide the evidence for fusion transcripts (use --extract_fusion_reads)
	perform 'in silico validation' of fusion transcripts using FusionInspector ( --FusionInspector <inspect|validate> )
	de novo reconstruct fusion transcripts using Trinity (--denovo_reconstruct)


Version 1.0.0 (Feb 1, 2017)
	including dinucleotide splice sites in the report
	incorporate FFPM values whenever fastq reads are given, regardless of using the chimeric junction files direction.
	uses samtools to extract sequence regions from the genome, rather than putting the entire genome into memory.
	

Version 0.8.0 (July 28, 2016):
	FFPM stats computed correctly when using gzipped fastq files
	upgraded FusionFilter: better takes into account overlapping genes and no longer (inadvertently) filters them out as candidate paralogs.
	
Version 0.7.0 (Mar 5, 2016)
	Update to FusionFilter v0.1.0
	Require long double anchor support for those fusions only supported by breakpoint/split reads and no spanning fragments, reduces FP rate.

Version 0.6.0 (Dec 16, 2015)
	including FFPM calculations in output summary.

Version 0.5.4 (Nov, 10, 2015)
	update to FusionFilter, no 2-pass in genome-generate function

Version 0.5.3 (Nov, 6, 2015)
	removed duplicate PE alignments supporting fusions, decreases FP rate dramatically on samples w/ high PCR dups, w/ little effect on other 'good' samples w/ low DUP rate.

Version 0.5.2 (Oct 26, 2016)
	Bugfix for paired cigar-string alignment parsing leading to proper grouping of junction counts.

Version 0.5.1 (Oct 10, 2015)
     added back capability to run STAR-Fusion from an existing Chimeric.out.junctions file from an earlier STAR run.
     Use parameter:  --chimeric_junction|J or (--left_fq, --right_fq)
