分割後のPythonでの一貫性のないインデント

それはうまくいくはずです：

import re #Regex may be the easiest way to split that line

with open(infile) as in_f, open(outfile,'w') as out_f:
    f = (i for i in in_f if i.rstrip()) #iterate over non empty lines
    for line in f:
        _, k = line.split('\t', 1)
        x = re.findall(r'^1..100\t([+-])chr(\d+):(\d+)\.\.(\d+).+$',k)
        if not x:
            continue
        out_f.write(' '.join(x[0]) + '\n')