add user defined genome and allow the pipeline to run in offline environment#11
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Serine94209792 wants to merge 3 commits into
Open
add user defined genome and allow the pipeline to run in offline environment#11Serine94209792 wants to merge 3 commits into
Serine94209792 wants to merge 3 commits into
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Edit genome parameter to
readBam, allowing user-defined genome (BSgenome object). Now, the genome parameter can have two types of input: string or Bsgenome object. In the meanwhile, genome_label have more options:hg19,hg38,hg38-NCBI,user_define, whengenome_label = 'user_define', genome cannot beNULL, whengenome_label != 'user_define', genome parameter will be ignored.Add genome parameter to
writeMutTable, can be explicitly assigned the BSgenome or justNULL