SplitFusion 0.7.0

Removed code that adjust breakpoints using known exon boundaries.

SplitFusion 0.6.0

1. Support for snpEff annotation is added. Set the annotation software path (ie, --annovar) to the snpEff path. To use annovar as the annotation method, add "--AnnotationMethod annovar" to the command line and also set --annovar to the annovar path.
2. Support for GRCh37 genome (ie the hg19 genome but without "chr" in the chromosome names). To use it, simply add "--genomeVer hg19" to the command line. It will add "chr" to the chromosome name in all the output files after consolidated.bam.

SplitFusion 0.5.0

This is the version used for the related publication.
The changes are:

1. Terra Bio support with docker image based on slim-bullseye with mawk built-in. Sample WDL to run on Terra Bio is also included. Memory usage is also optimized for the Terra Bio environment.
2. Support for fusion partners when they are located on repeatitive regions, e.g. DUX4 in CIC-DUX4 fusion. This is configurable in the hg19_pseudogene.bed or hg38_pseudogene.bed files.
3. filter.gene-gene.txt now have many entries derived from our TCGA LUAD 517 sample runs to reduce false negatives.
4. Added known.priority.txt to allow preferential extraction of bam file for fusions containing genes specified in it.
5. Average read length of input fastq will be used to determine different set of default parameters to optimize for 2x50 reads data from TCGA.
6. read.through is now only limited to genes going on the same direction (bug fix for not calling ERBB2-PPP1R1B)
7. fusion breakpoints are now corrected by exon boundaries when the true breakpoint is intronic (bug fix)
8. Better annovar annotation by using annotate_variation.pl instead of table_annovar.pl. As a result, annovar.exon.cds.extraction.R is replaced by annovar.exon.cds.extraction.awk (bug fix)

SplitFusion 0.4.0

Now includes a Dockerfile that builds a docker image based on python:3.8-slim-buster. Slightly modified the code to accommodate the docker image. Fixed a bug when read name or chromosome name contains '-'.

SplitFusion 0.3.0

Now supports CIC-DUX4. It also fixes a bug when read names containing '-'

SplitFusion 0.1.0

Initial Release of SplitFusion that works for hg19.