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#ifndef theplu_yat_omic_bam_read_sequence_iterator |
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#define theplu_yat_omic_bam_read_sequence_iterator |
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|
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// $Id$ |
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/* |
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Copyright (C) 2023 Peter Johansson |
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This file is part of the yat library, https://dev.thep.lu.se/yat |
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|
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The yat library is free software; you can redistribute it and/or |
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modify it under the terms of the GNU General Public License as |
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published by the Free Software Foundation; either version 3 of the |
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License, or (at your option) any later version. |
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|
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The yat library is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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General Public License for more details. |
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|
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You should have received a copy of the GNU General Public License |
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along with yat. If not, see <https://www.gnu.org/licenses/>. |
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*/ |
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|
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#include <boost/iterator/iterator_facade.hpp> |
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#include <cstdint> |
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namespace theplu { |
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namespace yat { |
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namespace omic { |
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|
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// forward declaration |
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class BamRead; |
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/** |
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A small class holding a sequence base and corresponding base |
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quality. |
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|
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\since New in yat 0.21 |
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*/ |
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class BamReadSequenceQuality |
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{ |
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public: |
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/// construct a default object |
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BamReadSequenceQuality(void) = default; |
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/** |
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construct a BamReadSequenceQuality with base \c b and quality |
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\c q |
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*/ |
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BamReadSequenceQuality(char b, uint8_t q); |
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|
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/// \return base |
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const char& base(void) const; |
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/// \return quality |
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const uint8_t& qual(void) const; |
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|
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/// \return base |
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char& base(void); |
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/// \return quality |
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uint8_t& qual(void); |
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private: |
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char base_; |
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uint8_t qual_; |
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}; |
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/** |
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\relates BamReadSequenceQuality |
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|
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\return true if both base and quality are the same for \c lhs and |
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\c rhs |
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|
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\since New in yat 0.21 |
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*/ |
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bool operator==(const BamReadSequenceQuality& lhs, |
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const BamReadSequenceQuality& rhs); |
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/** |
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\brief class to iterate through the sequence of a BamRead |
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Iterator is a const random access iterator |
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\since New in yat 0.21 |
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*/ |
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class BamReadSequenceIterator |
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: public boost::iterator_facade< |
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BamReadSequenceIterator, const BamReadSequenceQuality, |
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std::random_access_iterator_tag |
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> |
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{ |
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public: |
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/** |
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\brief Default constructor |
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*/ |
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BamReadSequenceIterator(void); |
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/** |
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Creates an iterator pointing to the ith base (and quality). |
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*/ |
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explicit BamReadSequenceIterator(const BamRead& bam, size_t i=0); |
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private: |
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friend class boost::iterator_core_access; |
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void advance(BamReadSequenceIterator::difference_type); |
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void decrement(void); |
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BamReadSequenceIterator::reference dereference(void) const; |
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typename BamReadSequenceIterator::difference_type |
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distance_to(const BamReadSequenceIterator& other) const; |
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bool equal(const BamReadSequenceIterator& other) const; |
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void increment(void); |
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void update(void); |
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const BamRead* bam_; |
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size_t index_; |
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BamReadSequenceQuality value_; |
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}; |
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}}} |
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#endif |