path_FuGePrior_out=FuGePrior_out
path_to_scripts=Scripts
pegasus_out=Pegasus_output_file/pegasus.output.txt
path_to_oncofuse=path_to_oncofuse_jar
path_to_reference=REFERENCE/hg19/hg19.fa
chimerascan_out=ChimeraScan_out
defuse_out=deFuse_out
generic_out=genericTool_out
sample1=SRR064286 
sample2=SRR064287
sample3=SRR064438
sample4=SRR064439
sample5=SRR064440
sample6=SRR064441
reactive1=SRR064437
threshold=0.7
unann_string=AC0,AC1,AK,AD0,AL0,AL1,AL5,AL6,AP0,NCRNA,LL22NC,CTC,RNASE,HLA,BC0,AL6,BC1,LOC
min_split_overlapping=15
bp_extension=15
oncofuse_pathology=MES



