151 lines
5.0 KiB
C++
151 lines
5.0 KiB
C++
#include <cstdio>
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#include <cstring>
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#include "bwase.h"
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#include "bwa_gateway.h"
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BWA::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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{
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bns = bns_restore_core(ann_filename,amb_filename,pac_filename);
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bwts[0] = bwt_restore_bwt(forward_bwt_filename);
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bwt_restore_sa(forward_sa_filename, bwts[0]);
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bwts[1] = bwt_restore_bwt(reverse_bwt_filename);
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bwt_restore_sa(reverse_sa_filename, bwts[1]);
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load_default_options();
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}
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BWA::~BWA() {
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bwt_destroy(bwts[0]);
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bwt_destroy(bwts[1]);
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}
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void BWA::align(const char* bases, const unsigned read_length, Alignment*& alignments, unsigned& num_alignments)
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{
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bwa_seq_t* sequence = create_sequence();
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copy_bases_into_sequence(sequence, bases, read_length, true);
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// Calculate the suffix array interval for each sequence, storing the result in sequence.aln (and sequence.n_aln).
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// This method will destroy the contents of seq and rseq.
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bwa_cal_sa_reg_gap(0,bwts,1,sequence,&options);
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// Translate suffix array indices into exactly how many alignments have been found.
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bwa_aln2seq(sequence->n_aln,sequence->aln,sequence);
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// Calculate and refine the position for each alignment. This position may be inaccurate
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// if the read contains indels, etc. Refinement requires the original sequences in the proper order.
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copy_bases_into_sequence(sequence, bases, read_length, false);
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create_alignments(sequence, alignments, num_alignments);
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bwa_free_read_seq(1,sequence);
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}
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void BWA::load_default_options()
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{
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options.s_mm = 3;
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options.s_gapo = 11;
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options.s_gape = 4;
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options.mode = 3;
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options.indel_end_skip = 5;
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options.max_del_occ = 10;
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options.max_entries = 2000000;
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options.fnr = 0.04;
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options.max_diff = -1;
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options.max_gapo = 1;
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options.max_gape = 6;
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options.max_seed_diff = 2;
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options.seed_len = 2147483647;
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options.n_threads = 1;
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options.max_top2 = 30;
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options.trim_qual = 0;
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}
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/**
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* Create a sequence with a set of reasonable initial defaults.
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* Will leave seq and rseq empty.
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*/
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bwa_seq_t* BWA::create_sequence()
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{
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bwa_seq_t* sequence = new bwa_seq_t;
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sequence->tid = -1;
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sequence->name = 0;
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sequence->seq = NULL;
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sequence->rseq = NULL;
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sequence->qual = 0;
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sequence->aln = 0;
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sequence->md = 0;
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sequence->cigar = NULL;
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sequence->n_cigar = 0;
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return sequence;
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}
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void BWA::copy_bases_into_sequence(bwa_seq_t* sequence, const char* bases, unsigned read_length, bool reverse)
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{
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// seq, rseq will ultimately be freed by bwa_cal_sa_reg_gap
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sequence->seq = new ubyte_t[read_length];
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sequence->rseq = new ubyte_t[read_length];
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for(unsigned i = 0; i < read_length; i++) sequence->seq[i] = nst_nt4_table[(unsigned)bases[i]];
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memcpy(sequence->rseq,sequence->seq,read_length);
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if(reverse) {
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seq_reverse(read_length,sequence->seq,0);
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seq_reverse(read_length,sequence->rseq,1);
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}
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sequence->full_len = sequence->len = read_length;
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}
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void BWA::create_alignments(bwa_seq_t* sequence, Alignment*& alignments, unsigned& num_alignments) {
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num_alignments = 0;
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for(unsigned i = 0; i < (unsigned)sequence->n_aln; i++)
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num_alignments += (sequence->aln + i)->l - (sequence->aln + i)->k + 1;
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alignments = new Alignment[num_alignments];
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unsigned alignment_idx = 0;
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// backup existing alignment blocks.
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bwt_aln1_t* alignment_blocks = sequence->aln;
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int num_alignment_blocks = sequence->n_aln;
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for(unsigned alignment_block_idx = 0; alignment_block_idx < (unsigned)num_alignment_blocks; alignment_block_idx++) {
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// Stub in a 'working' alignment block, so that only the desired alignment is local-aligned.
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const bwt_aln1_t* alignment_block = alignment_blocks + alignment_block_idx;
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bwt_aln1_t working_alignment_block = *alignment_block;
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// Loop through all alignments, aligning each one individually.
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for(unsigned sa_idx = alignment_block->k; sa_idx <= alignment_block->l; sa_idx++) {
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working_alignment_block.k = working_alignment_block.l = sa_idx;
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sequence->aln = &working_alignment_block;
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sequence->n_aln = 1;
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// Calculate the local alignment.
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bwa_cal_pac_pos_core(bwts[0],bwts[1],sequence,options.max_diff,options.fnr);
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bwa_refine_gapped(bns, 1, sequence, 0, NULL);
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// Copy the local alignment data into the alignment object.
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Alignment& alignment = *(alignments + alignment_idx);
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alignment.type = sequence->type;
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bns_coor_pac2real(bns, sequence->pos, pos_end(sequence) - sequence->pos, &alignment.contig);
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alignment.pos = sequence->pos - bns->anns[alignment.contig].offset + 1;
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alignment.negative_strand = sequence->strand;
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alignment.cigar = sequence->cigar;
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alignment.n_cigar = sequence->n_cigar;
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alignment.mapQ = sequence->mapQ;
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alignment_idx++;
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}
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}
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// Restore original alignment blocks.
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sequence->aln = alignment_blocks;
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sequence->n_aln = num_alignment_blocks;
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}
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