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utils.h
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27 
28 #pragma once
29 
30 #include <nvbio/basic/packedstream.h>
31 #include <nvbio/alignment/sink.h>
32 
33 namespace nvbio {
34 namespace aln {
35 
38 
41 
46 template <typename aligner_type> struct checkpoint_storage_type {
47  typedef null_type type;
48 };
49 template <AlignmentType TYPE, typename algorithm_tag> struct checkpoint_storage_type< EditDistanceAligner<TYPE,algorithm_tag> > { typedef int16 type; };
50 template <AlignmentType TYPE, typename scoring_type, typename algorithm_tag> struct checkpoint_storage_type< HammingDistanceAligner<TYPE,scoring_type,algorithm_tag> > { typedef int16 type; };
51 template <AlignmentType TYPE, typename scoring_type, typename algorithm_tag> struct checkpoint_storage_type< SmithWatermanAligner<TYPE,scoring_type,algorithm_tag> > { typedef int16 type; };
52 template <AlignmentType TYPE, typename scoring_type, typename algorithm_tag> struct checkpoint_storage_type< GotohAligner<TYPE,scoring_type,algorithm_tag> > { typedef short2 type; };
53 
58 template <typename aligner_type> struct column_storage_type {
59  typedef null_type type;
60 };
61 template <AlignmentType TYPE, typename algorithm_tag> struct column_storage_type< EditDistanceAligner<TYPE,algorithm_tag> > { typedef int16 type; };
62 template <AlignmentType TYPE, typename scoring_type, typename algorithm_tag> struct column_storage_type< HammingDistanceAligner<TYPE,scoring_type,algorithm_tag> > { typedef int16 type; };
63 template <AlignmentType TYPE, typename scoring_type, typename algorithm_tag> struct column_storage_type< SmithWatermanAligner<TYPE,scoring_type,algorithm_tag> > { typedef int16 type; };
64 template <AlignmentType TYPE, typename scoring_type, typename algorithm_tag> struct column_storage_type< GotohAligner<TYPE,scoring_type,algorithm_tag> > { typedef short2 type; };
65 
71 template <typename aligner_type> struct direction_vector_traits {
72  static const uint32 BITS = 2;
73 };
74 
80 template <AlignmentType TYPE, typename scoring_type, typename algorithm_tag> struct direction_vector_traits<GotohAligner<TYPE,scoring_type,algorithm_tag> > {
81  static const uint32 BITS = 4;
82 };
83 
85 
88 
92 struct SimpleSmithWatermanScheme
93 {
94  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE SimpleSmithWatermanScheme() {}
95  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE SimpleSmithWatermanScheme(
96  const int32 match, const int32 mm, const int32 del, const int32 ins) :
97  m_match(match), m_mismatch(mm), m_deletion(del), m_insertion(ins) {}
98 
99  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 match(const uint8 q = 0) const { return m_match; };
100  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 mismatch(const uint8 q = 0) const { return m_mismatch; };
101  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 mismatch(const uint8 a, const uint8 b, const uint8 q = 0) const { return m_mismatch; };
102  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 deletion() const { return m_deletion; };
103  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 insertion() const { return m_insertion; };
104 
105  int32 m_match;
106  int32 m_mismatch;
107  int32 m_deletion;
108  int32 m_insertion;
109 };
110 
114 struct SimpleGotohScheme
115 {
116  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE SimpleGotohScheme() {}
117  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE SimpleGotohScheme(
118  const int32 match, const int32 mm, const int32 gap_open, const int32 gap_ext) :
119  m_match(match), m_mismatch(mm), m_gap_open(gap_open), m_gap_ext(gap_ext) {}
120 
121  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 match(const uint8 q = 0) const { return m_match; };
122  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 mismatch(const uint8 q = 0) const { return m_mismatch; };
123  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 mismatch(const uint8 a, const uint8 b, const uint8 q = 0) const { return m_mismatch; };
124  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 substitution(const uint32 r_i, const uint32 q_j, const uint8 r, const uint8 q, const uint8 qq = 0) const { return q == r ? m_match : m_mismatch; };
125  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 pattern_gap_open() const { return m_gap_open; };
126  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 pattern_gap_extension() const { return m_gap_ext; };
127  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 text_gap_open() const { return m_gap_open; };
128  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 text_gap_extension() const { return m_gap_ext; };
129 
130  int32 m_match;
131  int32 m_mismatch;
132  int32 m_gap_open;
133  int32 m_gap_ext;
134 };
135 
140 template <AlignmentType TYPE, typename scoring_scheme_type, typename algorithm_tag>
141 NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
142 uint32 max_pattern_gaps(
143  const HammingDistanceAligner<TYPE,scoring_scheme_type,algorithm_tag>& aligner,
144  int32 min_score,
145  int32 pattern_len);
146 
151 template <AlignmentType TYPE, typename scoring_scheme_type, typename algorithm_tag>
152 NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
153 uint32 max_text_gaps(
154  const HammingDistanceAligner<TYPE,scoring_scheme_type, algorithm_tag>& aligner,
155  int32 min_score,
156  int32 pattern_len);
157 
162 template <AlignmentType TYPE, typename scoring_scheme_type, typename algorithm_tag>
163 NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
164 uint32 max_pattern_gaps(
165  const SmithWatermanAligner<TYPE,scoring_scheme_type,algorithm_tag>& aligner,
166  int32 min_score,
167  int32 pattern_len);
168 
173 template <AlignmentType TYPE, typename scoring_scheme_type, typename algorithm_tag>
174 NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
175 uint32 max_text_gaps(
176  const SmithWatermanAligner<TYPE,scoring_scheme_type, algorithm_tag>& aligner,
177  int32 min_score,
178  int32 pattern_len);
179 
184 template <AlignmentType TYPE, typename scoring_scheme_type, typename algorithm_tag>
185 NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
186 uint32 max_pattern_gaps(
187  const GotohAligner<TYPE,scoring_scheme_type,algorithm_tag>& aligner,
188  int32 min_score,
189  int32 pattern_len);
190 
195 template <AlignmentType TYPE, typename scoring_scheme_type, typename algorithm_tag>
196 NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
197 uint32 max_text_gaps(
198  const GotohAligner<TYPE,scoring_scheme_type,algorithm_tag>& aligner,
199  int32 min_score,
200  int32 pattern_len);
201 
206 template <AlignmentType TYPE, typename algorithm_tag>
207 NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
208 uint32 max_pattern_gaps(
209  const EditDistanceAligner<TYPE,algorithm_tag>& aligner,
210  int32 min_score,
211  int32 pattern_len);
212 
217 template <AlignmentType TYPE, typename algorithm_tag>
218 NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
219 uint32 max_text_gaps(
220  const EditDistanceAligner<TYPE,algorithm_tag>& aligner,
221  int32 min_score,
222  int32 pattern_len);
223 
228 struct trivial_quality_string
229 {
230  static const uint32 SYMBOL_SIZE = 8u;
231 
232  typedef random_access_universal_iterator_tag iterator_category;
233  typedef uint8 value_type;
234  typedef uint8 reference;
235  typedef const uint8* pointer;
236  typedef int32 difference_type;
237  typedef uint32 index_type;
238  typedef trivial_quality_string iterator;
239  typedef trivial_quality_string const_iterator;
240  typedef trivial_quality_string forward_iterator;
241 
244  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
245  uint8 operator[] (const index_type i) const { return 0u; }
246 
249  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
250  uint8 operator* () const { return 0u; }
251 
254  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
255  trivial_quality_string& operator++ (){ return *this; }
256 
259  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
260  trivial_quality_string operator++ (int dummy) { return *this; }
261 
264  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
265  trivial_quality_string& operator-- (){ return *this; }
266 
269  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
270  trivial_quality_string operator-- (int dummy) { return *this; }
271 
274  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
275  iterator begin() const { return *this; }
276 };
277 
281 struct trivial_quality_string_set
282 {
283  typedef trivial_quality_string string_type;
284 
285  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
286  string_type operator[] (const uint32 i) const { return string_type(); }
287 };
288 
291 
292 } // namespace aln
293 } // namespace nvbio
294 
295 #include <nvbio/alignment/utils_inl.h>
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