Commit 319fbb23 authored by Rebecca E Batorsky's avatar Rebecca E Batorsky
Browse files

remove extra files

parent 3092856d
#!/bin/bash
infile=/Users/rbator01/Box/rebecca_documents/sdmmej_data/PolyGSeq.csv
indir=/Users/rbator01/Box/rebecca_documents/sdmmej_data/
search_radius=30
breakpoint=161
debug=0
reclass=${infile%.csv}_reclassified.csv
deletion=${infile%.csv}_deletion.txt
insertion=${infile%.csv}_insertion.txt
Rscript process_hifibr.R $infile $indir $search_radius $breakpoint $debug
cd deletion/
python SDMMEJDeletionProgram_cli.py -hi $reclass -del $deletion -n $breakpoint -out $indir
cd ../insertion/
Rscript INSERTION_PROGRAM.R $reclass $insertion $indir $breakpoint $search_radius
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