0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd
max
  Fri Sep 20 13:18:01 2024 -0700
Revert "more features to hubtools: search in both parent and subdirs, better docs"

This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.

diff --git src/hg/makeDb/cadd/caddToWig.py src/hg/makeDb/cadd/caddToWig.py
index 99bf4a1..0eb21ab 100644
--- src/hg/makeDb/cadd/caddToWig.py
+++ src/hg/makeDb/cadd/caddToWig.py
@@ -1,31 +1,30 @@
-import sys
 import subprocess
 
 def inputLineChunk():
     " yield all values at consecutive positions as a tuple (chrom, pos, list of (nucl, phred value)) "
     ## CADD GRCh37-v1.6 (c) University of Washington, Hudson-Alpha Institute for Biotechnology and Berlin Institute of Health 2013-2019. All rights reserved.
     #Chrom  Pos     Ref     Alt     RawScore        PHRED
     #1       10001   T       A       0.088260        4.066
     values = []
     firstChrom = None
     firstPos = None
     lastChrom = None
     lastPos = None
 
     #for line in gzip.open("whole_genome_SNVs.tsv.gz"):
-    for line in subprocess.Popen(['zcat', sys.argv[1]], stdout=subprocess.PIPE, encoding="ascii").stdout:
+    for line in subprocess.Popen(['zcat', "whole_genome_SNVs.tsv.gz"], 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])
         phred = float(phred)
 
         if firstPos is None:
             firstChrom = chrom
             firstPos = pos
 
         if chrom!=lastChrom or pos-lastPos > 1 and firstChrom is not None:
             yield firstChrom, firstPos, values
             firstPos, firstChrom = None, None