61 lines
1.4 KiB
C++
61 lines
1.4 KiB
C++
#ifndef BWA_GATEWAY
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#define BWA_GATEWAY
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#include <cstdio>
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#include "bntseq.h"
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#include "bwt.h"
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#include "bwtaln.h"
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class Alignment;
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class BWA {
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private:
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bntseq_t *bns;
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ubyte_t* reference;
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bwt_t* bwts[2];
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gap_opt_t options;
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void load_default_options();
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bwa_seq_t* create_sequence();
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void copy_bases_into_sequence(bwa_seq_t* sequence, const char* bases, const unsigned read_length);
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void create_alignments(bwa_seq_t* sequence, Alignment*& alignments, unsigned& num_alignments);
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public:
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BWA(const char* ann_filename,
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const char* amb_filename,
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const char* pac_filename,
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const char* forward_bwt_filename,
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const char* forward_sa_filename,
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const char* reverse_bwt_filename,
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const char* reverse_sa_filename);
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~BWA();
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// Parameterize the aligner.
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void set_max_edit_distance(float edit_distance);
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void set_max_gap_opens(int max_gap_opens);
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void set_max_gap_extensions(int max_gap_extensions);
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void set_disallow_indel_within_range(int indel_range);
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void set_mismatch_penalty(int penalty);
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void set_gap_open_penalty(int penalty);
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void set_gap_extension_penalty(int penalty);
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// Perform the alignment
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void align(const char* bases, const unsigned read_length, Alignment*& alignments, unsigned& num_alignments);
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};
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class Alignment {
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public:
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uint32_t type;
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int contig;
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bwtint_t pos;
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bool negative_strand;
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uint16_t *cigar;
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int n_cigar;
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uint32_t mapQ;
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};
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#endif // BWA_GATEWAY
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