do not use previous cstats if NaN is present

AmpliconSuite · Jul 22, 2022 · 568626a · 568626a
1 parent d0db133
commit 568626a
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/src/AmpliconArchitect.py b/src/AmpliconArchitect.py
@@ -26,6 +26,7 @@
 
 from time import time
 TSTART = time()
+import numpy as np
 import pysam
 import argparse
 import sys
@@ -178,7 +179,7 @@ def process(self, msg, kwargs):
                 cstats = tuple(map(float, ll[1:]))
                 if len(cstats) < 15 or int(round(cstats[11])) < args.pair_support_min:
                     cstats = None
-                elif cstats[13] != args.insert_sdevs or bamfile_filesize != int(cstats[14]):
+                elif cstats[13] != args.insert_sdevs or bamfile_filesize != int(cstats[14]) or any(np.isnan(cstats)):
                     cstats = None
 
     coverage_stats_file.close()

diff --git a/src/amplified_intervals.py b/src/amplified_intervals.py
@@ -107,7 +107,7 @@
             bamfile_filesize = os.path.getsize(bamfile_pathname)
             if ll[0] == os.path.abspath(bamfile_pathname):
                 cstats = tuple(map(float, ll[1:]))
-                if len(cstats) < 15 or cstats[13] != 3 or bamfile_filesize != int(cstats[14]):
+                if len(cstats) < 15 or cstats[13] != 3 or bamfile_filesize != int(cstats[14]) or any(np.isnan(cstats)):
                     cstats = None
 
         coverage_stats_file.close()