drop the old SAM writer
This commit is contained in:
Heng Li
parent
0b0455ca51
commit
26f4c704ed
148
bwamem.c
148
bwamem.c
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@ -607,113 +607,6 @@ static inline int infer_bw(int l1, int l2, int score, int a, int q, int r)
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return w;
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}
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void bwa_hit2sam(kstring_t *str, const int8_t mat[25], int q, int r, int w, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, const bwahit_t *p_, int is_hard, const bwahit_t *m)
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{
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#define is_mapped(x) ((x)->rb >= 0 && (x)->rb < (x)->re && (x)->re <= bns->l_pac<<1)
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int score, n_cigar, is_rev = 0, rid, mid, copy_mate = 0, NM = -1;
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uint32_t *cigar = 0;
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int64_t pos = -1;
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bwahit_t ptmp, *p = &ptmp;
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if (!p_) { // in this case, generate an unmapped alignment
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memset(&ptmp, 0, sizeof(bwahit_t));
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ptmp.rb = ptmp.re = -1;
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} else ptmp = *p_;
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p->flag |= m? 1 : 0; // is paired in sequencing
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p->flag |= !is_mapped(p)? 4 : 0; // is mapped
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p->flag |= m && !is_mapped(m)? 8 : 0; // is mate mapped
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if (m && !is_mapped(p) && is_mapped(m)) {
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p->rb = m->rb; p->re = m->re; p->qb = 0; p->qe = s->l_seq;
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copy_mate = 1;
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}
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p->flag |= p->rb >= bns->l_pac? 0x10 : 0; // is reverse strand
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p->flag |= m && m->rb >= bns->l_pac? 0x20 : 0; // is mate on reverse strand
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if (is_mapped(p) && m && !is_mapped(m) && (p->flag&0x10)) p->flag |= 0x20; // if mate is unmapped, it takes the strand of the current read
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kputs(s->name, str); kputc('\t', str);
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if (is_mapped(p)) { // has a coordinate, no matter whether it is mapped or copied from the mate
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int sam_flag = p->flag&0xff; // the flag that will be outputed to SAM; it is not always the same as p->flag
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if (p->flag&0x10000) sam_flag |= 0x100;
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if (!copy_mate) {
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int w2;
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w2 = infer_bw(p->qe - p->qb, p->re - p->rb, p->score, mat[0], q, r);
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w2 = w2 < w? w2 : w;
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cigar = bwa_gen_cigar(mat, q, r, w2, bns->l_pac, pac, p->qe - p->qb, (uint8_t*)&s->seq[p->qb], p->rb, p->re, &score, &n_cigar, &NM);
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p->flag |= n_cigar == 0? 4 : 0; // FIXME: check why this may happen (this has already happened)
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} else n_cigar = 0, cigar = 0;
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pos = bns_depos(bns, p->rb < bns->l_pac? p->rb : p->re - 1, &is_rev);
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bns_cnt_ambi(bns, pos, p->re - p->rb, &rid);
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kputw(sam_flag, str); kputc('\t', str);
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kputs(bns->anns[rid].name, str); kputc('\t', str); kputuw(pos - bns->anns[rid].offset + 1, str); kputc('\t', str);
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kputw(p->qual, str); kputc('\t', str);
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if (n_cigar) {
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int i, clip5, clip3;
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clip5 = is_rev? s->l_seq - p->qe : p->qb;
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clip3 = is_rev? p->qb : s->l_seq - p->qe;
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if (clip5) { kputw(clip5, str); kputc("SH"[(is_hard!=0)], str); }
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for (i = 0; i < n_cigar; ++i) {
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kputw(cigar[i]>>4, str); kputc("MIDSH"[cigar[i]&0xf], str);
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}
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if (clip3) { kputw(clip3, str); kputc("SH"[(is_hard!=0)], str); }
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} else kputc('*', str);
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} else { // no coordinate
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kputw(p->flag, str);
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kputs("\t*\t0\t0\t*", str);
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rid = -1;
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}
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if (m && is_mapped(m)) { // then print mate pos and isize
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pos = bns_depos(bns, m->rb < bns->l_pac? m->rb : m->re - 1, &is_rev);
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bns_cnt_ambi(bns, pos, m->re - m->rb, &mid);
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kputc('\t', str);
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if (mid == rid) kputc('=', str);
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else kputs(bns->anns[mid].name, str);
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kputc('\t', str); kputuw(pos - bns->anns[mid].offset + 1, str);
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kputc('\t', str);
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if (mid == rid) {
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int64_t p0 = p->rb < bns->l_pac? p->rb : (bns->l_pac<<1) - 1 - p->rb;
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int64_t p1 = m->rb < bns->l_pac? m->rb : (bns->l_pac<<1) - 1 - m->rb;
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kputw(-(p0 - p1 + (p0 > p1? 1 : p0 < p1? -1 : 0)), str);
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} else kputw(0, str);
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kputc('\t', str);
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} else if (m && is_mapped(p)) { // then copy the position
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kputsn("\t=\t", 3, str);
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kputuw(pos - bns->anns[rid].offset + 1, str);
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kputsn("\t0\t", 3, str);
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} else kputsn("\t*\t0\t0\t", 7, str);
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if (p->flag&0x100) { // for secondary alignments, don't write SEQ and QUAL
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kputsn("*\t*", 3, str);
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} else if (!(p->flag&0x10)) { // print SEQ and QUAL, the forward strand
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int i, qb = 0, qe = s->l_seq;
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if (!(p->flag&4) && is_hard) qb = p->qb, qe = p->qe;
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ks_resize(str, str->l + (qe - qb) + 1);
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for (i = qb; i < qe; ++i) str->s[str->l++] = "ACGTN"[(int)s->seq[i]];
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kputc('\t', str);
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if (s->qual) { // printf qual
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ks_resize(str, str->l + (qe - qb) + 1);
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for (i = qb; i < qe; ++i) str->s[str->l++] = s->qual[i];
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str->s[str->l] = 0;
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} else kputc('*', str);
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} else { // the reverse strand
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int i, qb = 0, qe = s->l_seq;
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if (!(p->flag&4) && is_hard) qb = p->qb, qe = p->qe;
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ks_resize(str, str->l + (qe - qb) + 1);
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for (i = qe-1; i >= qb; --i) str->s[str->l++] = "TGCAN"[(int)s->seq[i]];
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kputc('\t', str);
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if (s->qual) { // printf qual
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ks_resize(str, str->l + (qe - qb) + 1);
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for (i = qe-1; i >= qb; --i) str->s[str->l++] = s->qual[i];
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str->s[str->l] = 0;
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} else kputc('*', str);
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}
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if (NM >= 0) { kputsn("\tNM:i:", 6, str); kputw(NM, str); }
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if (p->score >= 0) { kputsn("\tAS:i:", 6, str); kputw(p->score, str); }
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if (p->sub >= 0) { kputsn("\tXS:i:", 6, str); kputw(p->sub, str); }
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if (bwa_rg_id[0]) { kputsn("\tRG:Z:", 6, str); kputs(bwa_rg_id, str); }
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if (s->comment) { kputc('\t', str); kputs(s->comment, str); }
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kputc('\n', str);
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free(cigar);
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#undef is_mapped
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}
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static inline int get_rlen(int n_cigar, const uint32_t *cigar)
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{
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int k, l;
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@ -834,46 +727,6 @@ int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a)
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return mapq;
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}
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void mem_alnreg2hit(const mem_alnreg_t *a, bwahit_t *h)
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{
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h->rb = a->rb; h->re = a->re; h->qb = a->qb; h->qe = a->qe;
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h->score = a->score;
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h->sub = a->secondary >= 0? -1 : a->sub > a->csub? a->sub : a->csub;
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h->qual = 0; // quality unset
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h->flag = a->secondary >= 0? 0x100 : 0; // only the "secondary" bit is set
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}
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void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const bwahit_t *m)
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{
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int k;
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kstring_t str;
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str.l = str.m = 0; str.s = 0;
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if (a->n > 0 && a->a[0].score >= opt->T) {
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int mapq0 = -1;
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for (k = 0; k < a->n; ++k) {
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bwahit_t h;
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mem_alnreg_t *p = &a->a[k];
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if (p->score < opt->T) continue;
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if (p->secondary >= 0 && !(opt->flag&MEM_F_ALL)) continue;
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if (p->secondary >= 0 && p->score < a->a[p->secondary].score * .5) continue;
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mem_alnreg2hit(p, &h);
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bwa_fix_xref(opt->mat, opt->q, opt->r, opt->w, bns, pac, (uint8_t*)s->seq, &h.qb, &h.qe, &h.rb, &h.re);
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h.flag |= extra_flag;
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if ((opt->flag&MEM_F_NO_MULTI) && k && p->secondary < 0) h.flag |= 0x10000; // print the sequence, but flag as secondary (for Picard)
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h.qual = p->secondary >= 0? 0 : mem_approx_mapq_se(opt, p);
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if (k == 0) mapq0 = h.qual;
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else if (h.qual > mapq0) h.qual = mapq0;
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bwa_hit2sam(&str, opt->mat, opt->q, opt->r, p->w, bns, pac, s, &h, opt->flag&MEM_F_HARDCLIP, m);
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}
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} else {
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bwahit_t h;
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memset(&h, 0, sizeof(bwahit_t));
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h.rb = h.re = -1; h.flag = extra_flag;
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bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, s, &h, opt->flag&MEM_F_HARDCLIP, m);
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}
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s->sam = str.s;
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}
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void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m)
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{
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kstring_t str;
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@ -1024,7 +877,6 @@ static void *worker2(void *data)
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if (!(w->opt->flag&MEM_F_PE)) {
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for (i = w->start; i < w->n; i += w->step) {
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mem_mark_primary_se(w->opt, w->regs[i].n, w->regs[i].a);
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//mem_sam_se(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0);
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mem_reg2sam_se(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0);
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free(w->regs[i].a);
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}
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7
bwamem.h
7
bwamem.h
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@ -59,13 +59,6 @@ typedef struct {
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double avg, std;
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} mem_pestat_t;
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typedef struct { // TODO: This is an intermediate struct only. Better get rid of it.
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int64_t rb, re;
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int qb, qe, flag, qual;
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// optional info
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int score, sub;
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} bwahit_t;
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typedef struct { // This struct is only used for the convenience of API.
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int64_t pos; // forward strand 5'-end mapping position
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int rid; // reference sequence index in bntseq_t; <0 for unmapped
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@ -169,7 +169,6 @@ int mem_matesw(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const me
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int mem_pair(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const mem_pestat_t pes[4], bseq1_t s[2], mem_alnreg_v a[2], int id, int *sub, int *n_sub, int z[2])
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{
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extern void mem_alnreg2hit(const mem_alnreg_t *a, bwahit_t *h);
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pair64_v v, u;
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int r, i, k, y[4], ret; // y[] keeps the last hit
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kv_init(v); kv_init(u);
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