d6d6967d21a36badceed77f26525ec10c8540ebf
jcasper
  Tue Apr 5 17:40:55 2022 -0700
Updates to the DECIPHER pipeline, first for a manual build, refs #29130

diff --git src/hg/utils/otto/decipher/checkDecipher.sh src/hg/utils/otto/decipher/checkDecipher.sh
index cf3f945..6496a2a 100755
--- src/hg/utils/otto/decipher/checkDecipher.sh
+++ src/hg/utils/otto/decipher/checkDecipher.sh
@@ -40,30 +40,32 @@
     mkdir -p $today
 
     CNV=decipher-cnvs*.gpg
     SNV=decipher-snvs*.gpg
     cp -p $CNV $SNV $today
 
     cd $today
 
     # unpack the gpg encrypted file
     gpg --batch --passphrase-file "../gpg.pwd.new" ${CNV}
     gpg --batch --passphrase-file "../gpg.pwd.new" ${SNV}
 
     mkdir -p ${WORKDIR}/release/{hg38,hg19}
 
     # build the new DECIPHER track tables (builds bigBed for cnv's)
+    # THIS NEEDS TO CHANGE - NEW ARGUMENT IS JUST ONE VARIANT FILE FROM DECIPHER,
+    # BUT FIRST WE'LL NEED TO FIX THE FETCH SCRIPT
     ../buildDecipher `basename $CNV .gpg` `basename $SNV .gpg`
     ../validateDecipher.sh hg38
     #../validateDecipher.sh hg19
 
     # now install
     #for db in hg38 hg19
     for db in hg38
     do
         for i in `cat ../decipher.tables`
         do 
         n=$i"New"
         o=$i"Old"
         hgsqlSwapTables $db $n $i $o -dropTable3
         done
     done