Line 85 in metaSNV.py:

Bugfix, add if clause to check header of bam file.

Line 31 of src/collapse_coverages.py:
Sort strings instead of integers to make the code more general. Now keys can be string or number, when sorting strings we get the same result.

metaSNV.py

@@ -82,9 +82,10 @@ def get_header(args):
         line = line.rstrip().split('\t')
         if len(line) != 3:
             continue
-        line[1] = line[1].replace('SN:','')
-        line[2] = line[2].replace('LN:','')
-        f.write(line[1]+'\t1\t'+line[2]+'\n')
+        if line[0] == "@SQ":
+            line[1] = line[1].replace('SN:','')
+            line[2] = line[2].replace('LN:','')
+            f.write(line[1]+'\t1\t'+line[2]+'\n')
     f.close()
     args.ctg_len = args.project_dir + '/bed_header'
 
@@ -270,4 +271,3 @@ SOLUTION: make\n\n'''.format(basedir))
 
 if __name__ == '__main__':
     main()
-

src/collapse_coverages.py

@@ -28,7 +28,7 @@ def write_matrix(cov, header, ofile):
     out.write('TaxId\t')
     out.write('\t'.join([header for _ in bamfiles]))
     out.write('\n')
-    for taxid in sorted(avg_cov.keys(), key=int):
+    for taxid in sorted(avg_cov.keys()):
         c = cov[taxid]
         out.write('{}\t'.format(taxid))
         out.write('\t'.join([c[bf] for bf in bamfiles]))