def count_bams(infiles, outfile):
'''Count the number of alignments both pre and post dedup'''
outlines = []
for infile in infiles:
method = re.match("dedup_(.+).dir\/.+", infile)
if method:
method = method.groups()[0]
else:
method = "none"
track = re.search("([^/]+).bam", infile).groups()[0]
statement = '''samtools idxstats %(infile)s
| awk '{sum+=$3} END{print sum}' '''
count, _ = P.execute(statement)
outlines.append([method, track, count.strip()])
IOTools.writeLines(outfile,
outlines, header=["method", "track", "count"])
