1 # Copyright (C) 2013 Martin A. Hansen.
3 # This program is free software; you can redistribute it and/or
4 # modify it under the terms of the GNU General Public License
5 # as published by the Free Software Foundation; either version 2
6 # of the License, or (at your option) any later version.
8 # This program is distributed in the hope that it will be useful,
9 # but WITHOUT ANY WARRANTY; without even the implied warranty of
10 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
11 # GNU General Public License for more details.
13 # You should have received a copy of the GNU General Public License
14 # along with this program; if not, write to the Free Software
15 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
17 # http://www.gnu.org/copyleft/gpl.html
19 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
21 # This software is part of the Biopieces framework (www.biopieces.org).
23 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
28 def add_ambiguity_macro(inline_builder)
29 # Macro for matching nucleotides including ambiguity codes.
30 inline_builder.prefix %{
31 #define MATCH(A,B) ((bitmap[(int) A] & bitmap[(int) B]) != 0)
34 # Bitmap for matching nucleotides including ambiguity codes.
35 # For each value bits are set from the left: bit pos 1 for A,
36 # bit pos 2 for T, bit pos 3 for C, and bit pos 4 for G.
37 inline_builder.prefix %{
39 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
40 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
41 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
42 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
43 0, 1,14, 4,11, 0, 0, 8, 7, 0, 0,10, 0, 5,15, 0,
44 0, 0, 9,12, 2, 2,13, 3, 0, 6, 0, 0, 0, 0, 0, 0,
45 0, 1,14, 4,11, 0, 0, 8, 7, 0, 0,10, 0, 5,15, 0,
46 0, 0, 9,12, 2, 2,13, 3, 0, 6, 0, 0, 0, 0, 0, 0,
47 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
48 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
49 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
50 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
51 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
52 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
53 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
54 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0