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alignment_base_inl.h
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27 
28 #pragma once
29 
30 #include <nvbio/basic/types.h>
31 #include <nvbio/alignment/utils.h>
32 
33 namespace nvbio {
34 namespace aln {
35 
36 namespace priv {
37 
38 template <
39  typename aligner_type,
40  typename pattern_string,
41  typename qual_string,
42  typename text_string,
43  typename column_type>
44 struct alignment_score_dispatch {};
45 
46 template <
47  uint32 CHECKPOINTS,
48  typename aligner_type,
49  typename pattern_string,
50  typename qual_string,
51  typename text_string,
52  typename column_type>
53 struct alignment_checkpointed_dispatch {};
54 
55 template <
56  uint32 BAND_LEN,
57  typename aligner_type,
58  typename pattern_string,
59  typename qual_string,
60  typename text_string>
61 struct banded_alignment_score_dispatch {};
62 
63 template <
64  uint32 BAND_LEN,
65  uint32 CHECKPOINTS,
66  typename aligner_type,
67  typename pattern_string,
68  typename qual_string,
69  typename text_string>
70 struct banded_alignment_checkpointed_dispatch {};
71 
72 //
73 // Helper class for banded alignment
74 //
75 template <uint32 BAND_SIZE> struct Reference_cache
76 {
77  static const uint32 BAND_WORDS = (BAND_SIZE-1+7) >> 3;
78  typedef PackedStream<uint32*,uint8,2,false> type;
79 };
80 template <> struct Reference_cache<15u>
81 {
82  static const uint32 BAND_WORDS = 14u;
83  typedef uint32* type;
84 };
85 template <> struct Reference_cache<7u>
86 {
87  static const uint32 BAND_WORDS = 6u;
88  typedef uint32* type;
89 };
90 template <> struct Reference_cache<5u>
91 {
92  static const uint32 BAND_WORDS = 4u;
93  typedef uint32* type;
94 };
95 template <> struct Reference_cache<3u>
96 {
97  static const uint32 BAND_WORDS = 3u;
98  typedef uint32* type;
99 };
100 
101 } // namespace priv
102 
103 } // namespace alignment
104 } // namespace nvbio
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