NVBIO
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
output_priv.cpp
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 
28 #include <nvbio/io/output/output_priv.h>
29 #include <nvbio/io/output/output_batch.h>
30 #include <nvbio/basic/timer.h>
31 #include <nvbio/basic/vector.h>
32 
33 #include <stdio.h>
34 #include <stdarg.h>
35 
36 namespace nvbio {
37 namespace io {
38 
39 // extract alignment data for a given mate
40 // note that the mates can be different for the cigar, since mate 1 is always the anchor mate for cigars
41 AlignmentData get(HostOutputBatchSE& batch, const uint32 aln_id)
42 {
43  const uint32 read_id = batch.read_ids.size() ?
44  batch.read_ids[ aln_id ] : aln_id;
45 
46  return AlignmentData(&batch.alignments[aln_id],
47  batch.mapq[aln_id],
48  aln_id,
49  read_id,
50  batch.read_data,
51  &batch.cigar,
52  &batch.mds);
53 }
54 
55 // extract alignment data for a given mate
56 // note that the mates can be different for the cigar, since mate 1 is always the anchor mate for cigars
57 AlignmentData get_mate(HostOutputBatchPE& batch, const uint32 aln_id, const AlignmentMate mate)
58 {
59  const uint32 read_id = batch.read_ids.size() ?
60  batch.read_ids[ aln_id ] : aln_id;
61 
62  if (batch.alignments[0][aln_id].mate() == mate)
63  {
64  return AlignmentData(&batch.alignments[0][aln_id],
65  batch.mapq[0][aln_id],
66  aln_id,
67  read_id,
68  batch.read_data[ mate ],
69  &batch.cigar[0],
70  &batch.mds[0]);
71  }
72  else
73  {
74  return AlignmentData(&batch.alignments[1][aln_id],
75  batch.mapq[1][aln_id],
76  aln_id,
77  read_id,
78  batch.read_data[ mate ],
79  &batch.cigar[1],
80  &batch.mds[1]);
81  }
82 }
83 
84 // extract alignment data for the anchor mate
85 AlignmentData get_anchor_mate(HostOutputBatchPE& batch, const uint32 aln_id)
86 {
87  const uint32 read_id = batch.read_ids.size() ?
88  batch.read_ids[ aln_id ] : aln_id;
89  const uint32 mate = batch.alignments[0][aln_id].mate();
90 
91  return AlignmentData(&batch.alignments[0][aln_id],
92  batch.mapq[0][aln_id],
93  aln_id,
94  read_id,
95  batch.read_data[ mate ],
96  &batch.cigar[0],
97  &batch.mds[0]);
98 }
99 
100 // extract alignment data for the opposite mate
101 AlignmentData get_opposite_mate(HostOutputBatchPE& batch, const uint32 aln_id)
102 {
103  const uint32 read_id = batch.read_ids.size() ?
104  batch.read_ids[ aln_id ] : aln_id;
105  const uint32 mate = batch.alignments[1][aln_id].mate();
106 
107  return AlignmentData(&batch.alignments[1][aln_id],
108  batch.mapq[1][aln_id],
109  aln_id,
110  read_id,
111  batch.read_data[ mate ],
112  &batch.cigar[1],
113  &batch.mds[1]);
114 }
115 
116 } // namespace io
117 } // namespace nvbio
Generated on Wed Feb 25 2015 08:33:00 for NVBIO by   doxygen 1.8.4