Change pindel window size to 10M with a overlap change from 100K to 50K

snakecnv/detection.snk

@@ -54,13 +54,13 @@ def get_chr_batches(ref_file, chr):
     # Make ranges:
     groups = []
     start = 1
-    end = min(start + 19999999,  len_chr)
-    while (len_chr - end + 1 >= 19900000) or (len_chr + 1 == end):
+    end = min(start + 9999999,  len_chr)
+    while (len_chr - end + 1 >= 9950000) or (len_chr + 1 == end):
         groups.append((start, end))
         if len_chr + 1 == end:
             break
-        start = end - 99999
-        end = min(start + 19999999, len_chr + 1)
+        start = end - 9999
+        end = min(start + 9999999, len_chr + 1)
     last_group = (start, len_chr + 1)
     if last_group not in groups:
         groups.append(last_group)