removing izip and pysamstats import

snakecnv/bin/detect_regions_to_exclude.py

@@ -4,7 +4,6 @@ import argparse
 import os
 from tempfile import NamedTemporaryFile, mkdtemp
 from shutil import rmtree
-from itertools import izip
 
 import multiprocessing
 from functools import partial
@@ -12,7 +11,6 @@ from functools import partial
 import numpy as np
 
 import pysam
-import pysamstats
 import pybedtools
 
 from svrunner_utils import eprint
@@ -62,12 +60,12 @@ def get_bamcoverage(bamfile, fafile, chrom, window_size=500,
     return a
 
 
-def get_pysamstatsbamcoverage(bamfile, fafile, chrom, window_size=500):
-    mybam = pysam.AlignmentFile(bamfile)
-    a = pysamstats.load_binned("coverage", mybam,
-                               fafile=fafile,
-                               chrom=chrom,
-                               window_size=window_size)
+# def get_pysamstatsbamcoverage(bamfile, fafile, chrom, window_size=500):
+#     mybam = pysam.AlignmentFile(bamfile)
+#     a = pysamstats.load_binned("coverage", mybam,
+#                                fafile=fafile,
+#                                chrom=chrom,
+#                                window_size=window_size)
     return a