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r479: a bit code cleanup

This commit is contained in:
Heng Li 2017-10-05 16:15:14 -04:00
parent f266092699
commit e0baf1ad54
5 changed files with 19 additions and 16 deletions
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6
Makefile
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@ -68,7 +68,7 @@ chain.o: minimap.h mmpriv.h bseq.h kalloc.h
example.o: minimap.h kseq.h example.o: minimap.h kseq.h
format.o: kalloc.h mmpriv.h minimap.h bseq.h format.o: kalloc.h mmpriv.h minimap.h bseq.h
getopt.o: getopt.h getopt.o: getopt.h
hit.o: mmpriv.h minimap.h bseq.h kalloc.h hit.o: mmpriv.h minimap.h bseq.h kalloc.h khash.h
index.o: kthread.h bseq.h minimap.h mmpriv.h kvec.h kalloc.h khash.h index.o: kthread.h bseq.h minimap.h mmpriv.h kvec.h kalloc.h khash.h
kalloc.o: kalloc.h kalloc.o: kalloc.h
ksw2_extd2_sse.o: ksw2.h kalloc.h ksw2_extd2_sse.o: ksw2.h kalloc.h
@ -76,8 +76,8 @@ ksw2_exts2_sse.o: ksw2.h kalloc.h
ksw2_extz2_sse.o: ksw2.h kalloc.h ksw2_extz2_sse.o: ksw2.h kalloc.h
ksw2_ll_sse.o: ksw2.h kalloc.h ksw2_ll_sse.o: ksw2.h kalloc.h
main.o: bseq.h minimap.h mmpriv.h getopt.h main.o: bseq.h minimap.h mmpriv.h getopt.h
map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h khash.h
misc.o: minimap.h ksort.h misc.o: minimap.h ksort.h
pe.o: mmpriv.h minimap.h bseq.h pe.o: mmpriv.h minimap.h bseq.h kvec.h kalloc.h ksort.h
sdust.o: kalloc.h kdq.h kvec.h sdust.h sdust.o: kalloc.h kdq.h kvec.h sdust.h
sketch.o: kvec.h kalloc.h minimap.h sketch.o: kvec.h kalloc.h minimap.h

8
align.c
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@ -487,9 +487,11 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
regs[i].p->trans_strand = opt->flag&MM_F_SPLICE_FOR? 1 : 2; regs[i].p->trans_strand = opt->flag&MM_F_SPLICE_FOR? 1 : 2;
} }
if (r2.cnt > 0) regs = mm_insert_reg(&r2, i, &n_regs, regs); if (r2.cnt > 0) regs = mm_insert_reg(&r2, i, &n_regs, regs);
if (i > 0 && mm_align1_inv(km, opt, mi, qlen, qseq0, &regs[i-1], &regs[i], &r2, &ez)) { if (!(opt->flag&MM_F_SPLICE) && !(opt->flag&MM_F_SR) && i > 0) { // don't try inversion alignment for -xsplice or -xsr
regs = mm_insert_reg(&r2, i, &n_regs, regs); if (mm_align1_inv(km, opt, mi, qlen, qseq0, &regs[i-1], &regs[i], &r2, &ez)) {
++i; // skip the inserted INV alignment regs = mm_insert_reg(&r2, i, &n_regs, regs);
++i; // skip the inserted INV alignment
}
} }
} }
*n_regs_ = n_regs; *n_regs_ = n_regs;

2
format.c
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@ -254,7 +254,7 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
{ {
int flag, n_regs = n_regss[seg_idx]; int flag, n_regs = n_regss[seg_idx];
int this_rid = -1, this_pos = -1, this_rev = 0; int this_rid = -1, this_pos = -1, this_rev = 0;
const mm_reg1_t *regs = regss[seg_idx], *r_prev, *r_next; const mm_reg1_t *regs = regss[seg_idx], *r_prev = NULL, *r_next;
const mm_reg1_t *r = n_regs > 0 && reg_idx < n_regs && reg_idx >= 0? &regs[reg_idx] : NULL; const mm_reg1_t *r = n_regs > 0 && reg_idx < n_regs && reg_idx >= 0? &regs[reg_idx] : NULL;
// find the primary of the previous and the next segments, if they are mapped // find the primary of the previous and the next segments, if they are mapped

2
main.c
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@ -6,7 +6,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "getopt.h" #include "getopt.h"
#define MM_VERSION "2.2-r478-dirty" #define MM_VERSION "2.2-r479-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>

17
map.c
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@ -260,7 +260,7 @@ static mm_reg1_t *align_regs(const mm_mapopt_t *opt, const mm_idx_t *mi, void *k
void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname) void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
{ {
int i, j, max_gap_ref, rep_len, qlen_sum, n_regs0, rechain = 0; int i, j, max_gap_ref, rep_len, qlen_sum, n_regs0;
uint32_t hash; uint32_t hash;
int64_t n_a; int64_t n_a;
uint64_t *u; uint64_t *u;
@ -291,7 +291,8 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
a = mm_chain_dp(max_gap_ref, opt->max_gap, opt->bw, opt->max_chain_skip, opt->min_cnt, opt->min_chain_score, !!(opt->flag&MM_F_SPLICE), n_segs, n_a, a, &n_regs0, &u, b->km); a = mm_chain_dp(max_gap_ref, opt->max_gap, opt->bw, opt->max_chain_skip, opt->min_cnt, opt->min_chain_score, !!(opt->flag&MM_F_SPLICE), n_segs, n_a, a, &n_regs0, &u, b->km);
if ((opt->flag & MM_F_SR) && rep_len > 0) { if ((opt->flag & MM_F_SR) && rep_len > 0) {
if (n_regs0 > 0) { int rechain = 0;
if (n_regs0 > 0) { // test if the best chain has all the segments
int n_chained_segs = 1, max = 0, max_i = -1, max_off = -1, off = 0; int n_chained_segs = 1, max = 0, max_i = -1, max_off = -1, off = 0;
for (i = 0; i < n_regs0; ++i) { // find the best chain for (i = 0; i < n_regs0; ++i) { // find the best chain
if (max < u[i]>>32) max = u[i]>>32, max_i = i, max_off = off; if (max < u[i]>>32) max = u[i]>>32, max_i = i, max_off = off;
@ -322,22 +323,22 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
chain_post(opt, mi, b->km, qlen_sum, n_segs, qlens, &n_regs0, regs0, a); chain_post(opt, mi, b->km, qlen_sum, n_segs, qlens, &n_regs0, regs0, a);
if (n_segs == 1) { if (n_segs == 1) { // uni-segment
regs0 = align_regs(opt, mi, b->km, qlens[0], seqs[0], &n_regs0, regs0, a); regs0 = align_regs(opt, mi, b->km, qlens[0], seqs[0], &n_regs0, regs0, a);
mm_set_mapq(n_regs0, regs0, opt->min_chain_score, opt->a, rep_len); mm_set_mapq(n_regs0, regs0, opt->min_chain_score, opt->a, rep_len);
n_regs[0] = n_regs0, regs[0] = regs0; n_regs[0] = n_regs0, regs[0] = regs0;
} else { } else { // multi-segment
mm_seg_t *seg; mm_seg_t *seg;
seg = mm_seg_gen(b->km, hash, n_segs, qlens, n_regs0, regs0, n_regs, regs, a); seg = mm_seg_gen(b->km, hash, n_segs, qlens, n_regs0, regs0, n_regs, regs, a); // split fragment chain to separate segment chains
free(regs0); free(regs0);
for (i = 0; i < n_segs; ++i) { for (i = 0; i < n_segs; ++i) {
mm_set_parent(b->km, opt->mask_level, n_regs[i], regs[i], opt->a * 2 + opt->b); mm_set_parent(b->km, opt->mask_level, n_regs[i], regs[i], opt->a * 2 + opt->b); // update mm_reg1_t::parent
regs[i] = align_regs(opt, mi, b->km, qlens[i], seqs[i], &n_regs[i], regs[i], seg[i].a); regs[i] = align_regs(opt, mi, b->km, qlens[i], seqs[i], &n_regs[i], regs[i], seg[i].a);
mm_set_mapq(n_regs[i], regs[i], opt->min_chain_score, opt->a, rep_len); mm_set_mapq(n_regs[i], regs[i], opt->min_chain_score, opt->a, rep_len);
} }
mm_seg_free(b->km, n_segs, seg); mm_seg_free(b->km, n_segs, seg);
if (n_segs == 2 && opt->pe_ori >= 0 && (opt->flag&MM_F_CIGAR)) if (n_segs == 2 && opt->pe_ori >= 0 && (opt->flag&MM_F_CIGAR))
mm_pair(b->km, max_gap_ref, opt->pe_bonus, opt->a * 2 + opt->b, opt->a, qlens, n_regs, regs); mm_pair(b->km, max_gap_ref, opt->pe_bonus, opt->a * 2 + opt->b, opt->a, qlens, n_regs, regs); // pairing
} }
kfree(b->km, a); kfree(b->km, a);
@ -424,7 +425,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
for (i = 0; i < p->n_threads; ++i) for (i = 0; i < p->n_threads; ++i)
s->buf[i] = mm_tbuf_init(); s->buf[i] = mm_tbuf_init();
s->n_reg = (int*)calloc(3 * s->n_seq, sizeof(int)); s->n_reg = (int*)calloc(3 * s->n_seq, sizeof(int));
s->seg_off = s->n_reg + s->n_seq; s->seg_off = s->n_reg + s->n_seq; // seg_off and n_seg are allocated together with n_reg
s->n_seg = s->seg_off + s->n_seq; s->n_seg = s->seg_off + s->n_seq;
s->reg = (mm_reg1_t**)calloc(s->n_seq, sizeof(mm_reg1_t*)); s->reg = (mm_reg1_t**)calloc(s->n_seq, sizeof(mm_reg1_t*));
for (i = 1, j = 0; i <= s->n_seq; ++i) for (i = 1, j = 0; i <= s->n_seq; ++i)