4057 |
31 Mar 21 |
peter |
1 |
#ifndef _theplu_yat_omic_bam_pair_buffer_ |
4057 |
31 Mar 21 |
peter |
2 |
#define _theplu_yat_omic_bam_pair_buffer_ |
4057 |
31 Mar 21 |
peter |
3 |
|
4057 |
31 Mar 21 |
peter |
// $Id$ |
4057 |
31 Mar 21 |
peter |
5 |
|
4057 |
31 Mar 21 |
peter |
6 |
/* |
4057 |
31 Mar 21 |
peter |
Copyright (C) 2021 Peter Johansson |
4057 |
31 Mar 21 |
peter |
8 |
|
4057 |
31 Mar 21 |
peter |
This file is part of the yat library, http://dev.thep.lu.se/yat |
4057 |
31 Mar 21 |
peter |
10 |
|
4057 |
31 Mar 21 |
peter |
The yat library is free software; you can redistribute it and/or |
4057 |
31 Mar 21 |
peter |
modify it under the terms of the GNU General Public License as |
4057 |
31 Mar 21 |
peter |
published by the Free Software Foundation; either version 3 of the |
4057 |
31 Mar 21 |
peter |
License, or (at your option) any later version. |
4057 |
31 Mar 21 |
peter |
15 |
|
4057 |
31 Mar 21 |
peter |
The yat library is distributed in the hope that it will be useful, |
4057 |
31 Mar 21 |
peter |
but WITHOUT ANY WARRANTY; without even the implied warranty of |
4057 |
31 Mar 21 |
peter |
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
4057 |
31 Mar 21 |
peter |
General Public License for more details. |
4057 |
31 Mar 21 |
peter |
20 |
|
4057 |
31 Mar 21 |
peter |
You should have received a copy of the GNU General Public License |
4057 |
31 Mar 21 |
peter |
along with yat. If not, see <http://www.gnu.org/licenses/>. |
4057 |
31 Mar 21 |
peter |
23 |
*/ |
4057 |
31 Mar 21 |
peter |
24 |
|
4057 |
31 Mar 21 |
peter |
25 |
#include "BamRead.h" |
4057 |
31 Mar 21 |
peter |
26 |
|
4057 |
31 Mar 21 |
peter |
27 |
#include <yat/utility/SortedBuffer.h> |
4057 |
31 Mar 21 |
peter |
28 |
#include <yat/utility/yat_assert.h> |
4057 |
31 Mar 21 |
peter |
29 |
|
4057 |
31 Mar 21 |
peter |
30 |
namespace theplu { |
4057 |
31 Mar 21 |
peter |
31 |
namespace yat { |
4057 |
31 Mar 21 |
peter |
32 |
namespace omic { |
4057 |
31 Mar 21 |
peter |
33 |
|
4057 |
31 Mar 21 |
peter |
34 |
/** |
4057 |
31 Mar 21 |
peter |
Bam read pairs can be added to this class and it handles to sort |
4057 |
31 Mar 21 |
peter |
reads (according to the genomic position, see BamLessPos) and |
4057 |
31 Mar 21 |
peter |
copy to an output iterator. It is assumed that the inserted read |
4057 |
31 Mar 21 |
peter |
pairs are sorted with respect to their first read. This can be |
4057 |
31 Mar 21 |
peter |
accomplished with e.g. BapPairIterator2. |
4057 |
31 Mar 21 |
peter |
40 |
|
4057 |
31 Mar 21 |
peter |
\see BamPairIterator2 |
4057 |
31 Mar 21 |
peter |
42 |
|
4057 |
31 Mar 21 |
peter |
\since New in yat 0.19 |
4057 |
31 Mar 21 |
peter |
44 |
*/ |
4057 |
31 Mar 21 |
peter |
45 |
template<typename OutputIterator> |
4057 |
31 Mar 21 |
peter |
46 |
class BamPairBuffer |
4057 |
31 Mar 21 |
peter |
47 |
{ |
4057 |
31 Mar 21 |
peter |
48 |
public: |
4057 |
31 Mar 21 |
peter |
49 |
/** |
4057 |
31 Mar 21 |
peter |
\brief Constructor |
4057 |
31 Mar 21 |
peter |
51 |
|
4057 |
31 Mar 21 |
peter |
Creates a buffer that flush elements to \c out. |
4057 |
31 Mar 21 |
peter |
53 |
*/ |
4057 |
31 Mar 21 |
peter |
54 |
BamPairBuffer(OutputIterator out) |
4057 |
31 Mar 21 |
peter |
55 |
: buffer_(out) {} |
4057 |
31 Mar 21 |
peter |
56 |
|
4057 |
31 Mar 21 |
peter |
57 |
/** |
4057 |
31 Mar 21 |
peter |
Position of \c first read is less (or equal) than position of |
4057 |
31 Mar 21 |
peter |
\c second. |
4057 |
31 Mar 21 |
peter |
60 |
|
4057 |
31 Mar 21 |
peter |
It is assumed that read pairs are pushed in a sorted order such |
4057 |
31 Mar 21 |
peter |
that first is not less than the previous first. |
4057 |
31 Mar 21 |
peter |
63 |
*/ |
4057 |
31 Mar 21 |
peter |
64 |
void push(const BamRead& first, const BamRead& second) |
4057 |
31 Mar 21 |
peter |
65 |
{ |
4057 |
31 Mar 21 |
peter |
// first <= second within each pair |
4057 |
31 Mar 21 |
peter |
67 |
YAT_ASSERT(BamLessPos()(second, first) == false); |
4057 |
31 Mar 21 |
peter |
// read pairs come sorted wrt first, i.e., all future ::first |
4057 |
31 Mar 21 |
peter |
// are greater (or equal) than current first, and thus all |
4057 |
31 Mar 21 |
peter |
// future reads are greater (or equal) than first. |
4057 |
31 Mar 21 |
peter |
71 |
buffer_.flush(first); |
4057 |
31 Mar 21 |
peter |
72 |
buffer_.push(first); |
4057 |
31 Mar 21 |
peter |
73 |
buffer_.push(second); |
4057 |
31 Mar 21 |
peter |
74 |
} |
4057 |
31 Mar 21 |
peter |
75 |
private: |
4057 |
31 Mar 21 |
peter |
76 |
utility::SortedBuffer<BamRead, OutputIterator, BamLessPos> buffer_; |
4057 |
31 Mar 21 |
peter |
77 |
}; |
4057 |
31 Mar 21 |
peter |
78 |
|
4057 |
31 Mar 21 |
peter |
79 |
}}} |
4057 |
31 Mar 21 |
peter |
80 |
#endif |