--- a/genetrack.py	Sun Nov 29 19:16:35 2015 -0500
+++ b/genetrack.py	Wed Dec 02 16:14:58 2015 -0500
@@ -9,6 +9,8 @@
 import os
 import genetrack_util
 
+CHUNK_SIZE = 10000000
+
 
 if __name__ == '__main__':
     parser = optparse.OptionParser()
@@ -19,7 +21,6 @@
     parser.add_option('-u', '--up_width', dest='up_width', type='int', default=10, help='Upstream width of called peaks.')
     parser.add_option('-d', '--down_width', dest='down_width', type='int', default=10, help='Downstream width of called peaks.')
     parser.add_option('-f', '--filter', dest='filter', type='int', default=3, help='Absolute read filter.')
-    parser.add_option('-c', '--chunk_size', dest='chunk_size', type='int', default=10, help='Size, in millions of base pairs.')
     options, args = parser.parse_args()
 
     os.mkdir('output')
@@ -39,7 +40,6 @@
         output_path = os.path.join('output', output_name)
         reader = csv.reader(open(input_path, 'rU'), delimiter='\t')
         writer = csv.writer(open(output_path, 'wt'), delimiter='\t')
-        chunk_size = options.chunk_size * 10 ** 6
         width = options.sigma * 5
         manager = genetrack_util.ChromosomeManager(reader)
         while not manager.done:
@@ -50,7 +50,7 @@
                 continue
             keys = genetrack_util.make_keys(data)
             lo, hi = genetrack_util.get_range(data)
-            for chunk in genetrack_util.get_chunks(lo, hi, size=chunk_size, overlap=width):
+            for chunk in genetrack_util.get_chunks(lo, hi, size=CHUNK_SIZE, overlap=width):
                 (slice_start, slice_end), process_bounds = chunk
                 window = genetrack_util.get_window(data, slice_start, slice_end, keys)
                 genetrack_util.process_chromosome(cname,