#!/bin/bash
set -beEu -o pipefail

deciphervarfile=$1

# Get canonical gene symbols
hgsql -Ne "select chrom,chromStart,chromEnd,geneSymbol from knownCanonical kc join kgXref kg on kc.transcript=kg.kgID" hg38 | sort -k1,1 -k2,2n > hg38.knownCanonical.genes

../processDecipher.py $deciphervarfile hg38.knownCanonical.genes decipherCnv.bed decipherSnvsNew.bed decipherSnvsRawNew.txt
bedSort decipherSnvsNew.bed decipherSnvsNew.bed
bedSort decipherCnv.bed decipherCnv.bed

hgLoadBed hg38 decipherSnvsNew decipherSnvsNew.bed
hgLoadSqlTab hg38 decipherSnvsRawNew ../decipherSnvsRaw.sql decipherSnvsRawNew.txt

bedToBigBed -extraIndex=name -tab -as=../decipherCnv.as -type=bed9+10 decipherCnv.bed /hive/data/genomes/hg38/chrom.sizes decipherCnv.bb
