# get raw data file from DECIPHER

cp $1  decipherRaw.txt -p

hgsql hg19 -e 'delete from decipherRaw'

hgsql hg19 -e \
'load data local infile "decipherRaw.txt" into table decipherRaw ignore 1 lines'

hgsql hg19 -N -e 'select "chr", chr, start-1, end, id from decipherRaw ' |\
sed -e 's/chr\t/chr/' |sort -u>j.tmp

# fix some out of range of entries
cat j.tmp|sed -e 's/243000000/242951149/' |\
sed -e 's/115090019/114142980/' >decipher.bed
rm j.tmp

# Load decipher table
hgLoadBed hg19 decipher decipher.bed

# Create knownToDecipher table
hgMapToGene -all hg19 decipher knownGene knownToDecipher

# Create knownCanonToDecipher table

hgsql hg19 -N -e \
'select d.* from knownToDecipher d, knownCanonical c where c.transcript=d.name' >knownCanonToDecipher.tab

hgsql hg19 -e 'delete from knownCanonToDecipher'
hgsql hg19 -e 'load data local infile "knownCanonToDecipher.tab" into table knownCanonToDecipher'


