variable name change peaktfile -> tfile, peakcfile -> cfile
-# Time-stamp: <2021-03-10 23:51:54 Tao Liu>
+# Time-stamp: <2022-02-22 17:26:52 Tao Liu>
"""Description: macs call
@@ -118,8 +118,8 @@ def run( args ):
error = options.error
peakbedfile = options.peakbed
- peaktfile = options.tfile
- peakcfile = options.cfile
+ tfile = options.tfile
+ cfile = options.cfile
top2allelesminr = options.top2allelesMinRatio
min_altallele_count = options.altalleleMinCount
max_allowed_ar = options.maxAR
@@ -146,9 +146,9 @@ def run( args ):
chrs = peaks.get_chr_names()
- tbam = BAMaccessor( peaktfile )
- if peakcfile:
- cbam = BAMaccessor( peakcfile )
+ tbam = BAMaccessor( tfile )
+ if cfile:
+ cbam = BAMaccessor( cfile )
assert tbam.get_chromosomes()[0] in cbam.get_chromosomes() or cbam.get_chromosomes()[0] in tbam.get_chromosomes(), Exception("It seems Treatment and Control BAM use different naming for chromosomes! Check headers of both files.")
#assert tbam.get_chromosomes() == cbam.get_chromosomes(), Exception("Treatment and Control BAM files have different orders of sorted chromosomes! Please check BAM Headers and re-sort BAM files.")
else:
