NVBIO
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
mapping_impl.h
Go to the documentation of this file.
1 /*
2  * nvbio
3  * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
4  *
5  * Redistribution and use in source and binary forms, with or without
6  * modification, are permitted provided that the following conditions are met:
7  * * Redistributions of source code must retain the above copyright
8  * notice, this list of conditions and the following disclaimer.
9  * * Redistributions in binary form must reproduce the above copyright
10  * notice, this list of conditions and the following disclaimer in the
11  * documentation and/or other materials provided with the distribution.
12  * * Neither the name of the NVIDIA CORPORATION nor the
13  * names of its contributors may be used to endorse or promote products
14  * derived from this software without specific prior written permission.
15  *
16  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
17  * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
18  * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
19  * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY
20  * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
21  * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
22  * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
23  * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
24  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
25  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
26  */
27 
31 
32 #pragma once
33 
41 #include <nvbio/io/utils.h>
47 #include <nvbio/basic/algorithms.h>
48 
49 namespace nvbio {
50 namespace bowtie2 {
51 namespace cuda {
52 
55 
74 
77 
81 template <typename BatchType, typename FMType, typename rFMType>
82 void map_whole_read_t(
83  const BatchType& read_batch, const FMType fmi, const rFMType rfmi,
85  uint8* reseed,
86  SeedHitDequeArrayDeviceView hits,
87  const ParamsPOD params,
88  const bool fw,
89  const bool rc);
90 
95 template <typename BatchType, typename FMType, typename rFMType>
96 void map_exact_t(
97  const BatchType& read_batch, const FMType fmi, const rFMType rfmi,
98  const uint32 retry,
100  uint8* reseed,
101  SeedHitDequeArrayDeviceView hits,
102  const ParamsPOD params,
103  const bool fw,
104  const bool rc);
105 
109 template <typename BatchType, typename FMType, typename rFMType>
110 void map_exact_t(
111  const BatchType& read_batch, const FMType fmi, const rFMType rfmi,
112  SeedHitDequeArrayDeviceView hits,
113  const uint2 seed_range,
114  const ParamsPOD params,
115  const bool fw,
116  const bool rc);
117 
122 template <typename BatchType, typename FMType, typename rFMType>
123 void map_case_pruning_t(
124  const BatchType& read_batch, const FMType fmi, const rFMType rfmi,
125  const uint32 retry,
127  uint8* reseed,
128  SeedHitDequeArrayDeviceView hits,
129  const ParamsPOD params,
130  const bool fw,
131  const bool rc);
132 
137 template <typename BatchType, typename FMType, typename rFMType>
138 void map_approx_t(
139  const BatchType& read_batch, const FMType fmi, const rFMType rfmi,
140  const uint32 retry,
142  uint8* reseed,
143  SeedHitDequeArrayDeviceView hits,
144  const ParamsPOD params,
145  const bool fw,
146  const bool rc);
147 
151 template <typename BatchType, typename FMType, typename rFMType>
152 void map_approx_t(
153  const BatchType& read_batch, const FMType fmi, const rFMType rfmi,
154  SeedHitDequeArrayDeviceView hits,
155  const uint2 seed_range,
156  const ParamsPOD params,
157  const bool fw,
158  const bool rc);
159 
163 template <typename BatchType, typename FMType, typename rFMType>
164 void map_t(
165  const BatchType& read_batch, const FMType fmi, const rFMType rfmi,
166  const uint32 retry,
168  uint8* reseed,
169  SeedHitDequeArrayDeviceView hits,
170  const ParamsPOD params,
171  const bool fw,
172  const bool rc);
173 
176 
177 } // namespace cuda
178 } // namespace bowtie2
179 } // namespace nvbio
180