382d7a0dacd948be55a2aa8548db7542a5e3335a
max
  Thu Feb 18 06:31:43 2021 -0800
fixing cadd deletions and inserts, refs #18492

diff --git src/hg/makeDb/cadd/caddToBed.py src/hg/makeDb/cadd/caddToBed.py
index d902ef4..e8b0171 100644
--- src/hg/makeDb/cadd/caddToBed.py
+++ src/hg/makeDb/cadd/caddToBed.py
@@ -1,36 +1,40 @@
 import sys
 import subprocess
 ## CADD GRCh38-v1.6 (c) University of Washington, Hudson-Alpha Institute for Biotechnology and Berlin Institute of Health 2013-2020. All rights reserved.
 #Chrom  Pos     Ref     Alt     RawScore        PHRED
 #1       10061   T       TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC        0.199964        3.123
 #1       10067   T       TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC      0.225348        3.416
 #1       10108   C       CA      0.390514        5.321
 
 insFh = open("ins.bed", "w")
 delFh = open("del.bed", "w")
 
 inFname = sys.argv[1]
 for line in subprocess.Popen(['zcat', inFname], stdout=subprocess.PIPE, encoding="ascii").stdout:
     if line.startswith("#"):
         continue
     row = line.rstrip("\n").split("\t")
     chrom, pos, ref, alt, raw, phred = row
     chrom = "chr"+chrom
     pos = int(row[1])-1
     phred = float(phred)
 
     if len(ref) < len(alt):
         # insertion
         insLen = len(alt)-1
         name = str(insLen)
         desc = "ins."+alt[1:]
         ofh = insFh
+        start = str(pos+1)
+        end = str(pos+1)
     else:
         delLen = len(ref)-1
         name = str(delLen)
         desc = "del."+ref[1:]
         ofh = delFh
+        start = str(pos+1)
+        end = str(pos+1+delLen)
 
-    bed = [chrom, str(pos), str(pos+1), name, str(round(phred)), ".", str(pos), str(pos+1), "0", desc, str(phred)]
+    bed = [chrom, start, end, name, str(round(phred)), ".", start, end, "0", desc, str(phred)]
     ofh.write("\t".join(bed))
     ofh.write("\n")