diff --git a/src/count_homopolymers.py b/src/count_homopolymers.py
deleted file mode 100755
index 8193535..0000000
--- a/src/count_homopolymers.py
+++ /dev/null
@@ -1,75 +0,0 @@
-#!/usr/bin/env python
-
-
-import sys
-import getopt
-from time import strftime
-import re
-
-
-def main():
-    infile = sys.argv[1]
-    # print strftime("%Y-%m-%d %H:%M:%S") + ": Start!"
-
-    with open(infile, 'r') as f:
-        for line in f:
-            new = line.strip().split()
-            ref = new[6]
-            new_line = next(f)
-            new = new_line.strip().split()
-            query = new[6]
-
-            i = 0
-            while i <= len(ref):
-                if i == 0:
-                    r_prev = ref[i]
-                    i += 1
-                    last_pos = [0, 1]
-                    continue
-                if i == len(ref) or (ref[i] != '-' and ref[i] != r_prev):
-                    j = last_pos[1] - 1
-                    while j >= 0 and query[j] == r_prev:
-                        j -= 1
-                    if j < last_pos[0]:
-                        last_pos[0] = j + 1
-
-                    j = last_pos[1]
-                    while j < len(ref) and query[j] == r_prev:
-                        j += 1
-                    if j > last_pos[1]:
-                        last_pos[1] = j
-
-                    if last_pos[1] - last_pos[0] >= 6:
-                        r_seq = ''.join(ref[last_pos[0]:last_pos[1]].split('-'))
-                        r_homo = re.findall(r_prev + '+', r_seq)
-                        r_len = max(len(h) for h in r_homo)
-
-                        q_seq = ''.join(query[last_pos[0]:last_pos[1]].split('-'))
-                        q_homo = re.findall(r_prev + '+', q_seq)
-                        q_len = max(len(h) for h in q_homo) if len(q_homo) != 0 else 0
-
-                        print ref[last_pos[0]:last_pos[1]], query[last_pos[0]:last_pos[1]], r_len, q_len
-
-                    if j == len(ref):
-                        break
-
-                    i = last_pos[1]
-                    while ref[i] == '-':
-                        i += 1
-                    last_pos[0] = i
-                    r_prev = ref[i]
-                    i += 1
-                    last_pos[1] = i
-
-                elif ref[i] == r_prev:
-                    last_pos[1] += 1
-                    i += 1
-                elif ref[i] == '-':
-                    i += 1
-
-    # print strftime("%Y-%m-%d %H:%M:%S") + ": Finished!"
-
-
-if __name__ == "__main__":
-    main()
-