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"""compute number of reads/alignments from BAM file
===================================================
This is a benchmarking utility script with limited functionality.
Compute simple flag stats on a BAM-file using
the pysam cython interface.
"""
import sys
import pysam
import pyximport
pyximport.install()
import _cython_flagstat
assert len(sys.argv) == 2, "USAGE: {} filename.bam".format(sys.argv[0])
is_paired, is_proper = _cython_flagstat.count(
pysam.AlignmentFile(sys.argv[1], "rb"))
print ("there are alignments of %i paired reads" % is_paired)
print ("there are %i proper paired alignments" % is_proper)
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