NVBIO
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
locate.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 
36 #include <nvbio/io/alignments.h>
37 
38 namespace nvbio {
39 namespace bowtie2 {
40 namespace cuda {
41 
42 template <typename ScoringScheme> struct BaseScoringPipelineState;
43 template <typename ScoringScheme> struct BestApproxScoringPipelineState;
44 
47 
62 
65 
73 template <typename BatchType, typename FMType, typename rFMType>
74 void locate(
75  const BatchType read_batch, const FMType fmi, const rFMType rfmi,
76  const uint32 in_count,
77  const uint32* idx_queue,
79  const ParamsPOD params);
80 
89 template <typename BatchType, typename FMType, typename rFMType>
90 void locate_init(
91  const BatchType read_batch, const FMType fmi, const rFMType rfmi,
92  const uint32 in_count,
93  const uint32* idx_queue,
95  const ParamsPOD params);
96 
105 template <typename BatchType, typename FMType, typename rFMType>
106 void locate_lookup(
107  const BatchType read_batch, const FMType fmi, const rFMType rfmi,
108  const uint32 in_count,
109  const uint32* idx_queue,
110  HitQueuesDeviceView hits,
111  const ParamsPOD params);
112 
119 template <typename ScoringScheme>
120 void locate_init(
122  const ParamsPOD params);
123 
130 template <typename ScoringScheme>
131 void locate_lookup(
133  const ParamsPOD params);
134 
138 template <typename index_iterator, typename flags_iterator>
139 void mark_straddling(
140  const uint32 in_count,
141  const uint32* idx_queue,
142  const uint32 reference_count,
143  const index_iterator reference_index,
144  HitQueuesDeviceView hits,
145  flags_iterator flags,
146  const ParamsPOD params);
147 
150 
151 } // namespace cuda
152 } // namespace bowtie2
153 } // namespace nvbio
154