r718: merge alnregs overlapping on both query/ref
This commit is contained in:
Heng Li
parent
a38b065642
commit
4e22270eba
50
bwamem.c
50
bwamem.c
|
|
@ -358,7 +358,7 @@ KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt)
|
|||
#define alnreg_hlt(a, b) ((a).score > (b).score || ((a).score == (b).score && (a).hash < (b).hash))
|
||||
KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt)
|
||||
|
||||
int mem_sort_and_dedup(int n, mem_alnreg_t *a, float mask_level_redun)
|
||||
int mem_sort_and_dedup2(int n, mem_alnreg_t *a, float mask_level_redun, int merge_bw)
|
||||
{
|
||||
int m, i, j;
|
||||
if (n <= 1) return n;
|
||||
|
|
@ -366,19 +366,39 @@ int mem_sort_and_dedup(int n, mem_alnreg_t *a, float mask_level_redun)
|
|||
for (i = 1; i < n; ++i) {
|
||||
mem_alnreg_t *p = &a[i];
|
||||
if (p->rb >= a[i-1].re) continue;
|
||||
for (j = i - 1; j >= 0 && p->rb < a[j].re; --j) {
|
||||
for (j = i - 1; j >= 0 && p->rid == a[j].rid && p->rb < a[j].re; --j) {
|
||||
mem_alnreg_t *q = &a[j];
|
||||
int64_t or, oq, mr, mq;
|
||||
int is_merged = 0;
|
||||
if (q->qe == q->qb) continue; // a[j] has been excluded
|
||||
or = q->re - p->rb; // overlap length on the reference
|
||||
oq = q->qb < p->qb? q->qe - p->qb : p->qe - q->qb; // overlap length on the query
|
||||
mr = q->re - q->rb < p->re - p->rb? q->re - q->rb : p->re - p->rb; // min ref len in alignment
|
||||
mq = q->qe - q->qb < p->qe - p->qb? q->qe - q->qb : p->qe - p->qb; // min qry len in alignment
|
||||
if (or > mask_level_redun * mr && oq > mask_level_redun * mq) { // one of the hits is redundant
|
||||
if (p->score < q->score) {
|
||||
p->qe = p->qb;
|
||||
break;
|
||||
} else q->qe = q->qb;
|
||||
if (merge_bw > 0 && q->qb < p->qb && q->qe < p->qe && q->re < p->re) {
|
||||
int flag = 0;
|
||||
int64_t l1, l2;
|
||||
l1 = p->qb - q->qb, l2 = p->rb - q->rb;
|
||||
if (l1 - l2 < merge_bw && l2 - l1 < merge_bw) ++flag;
|
||||
l1 = p->qe - q->qe, l2 = p->re - q->re;
|
||||
if (l1 - l2 < merge_bw && l2 - l1 < merge_bw) ++flag;
|
||||
if (flag == 2) { // merge q into p
|
||||
mem_alnreg_t t = *p;
|
||||
*p = *q;
|
||||
p->qe = t.qe, p->re = t.re;
|
||||
p->score = p->score > t.score? p->score : t.score;
|
||||
p->w = p->w > t.w? p->w : t.w;
|
||||
q->qb = q->qe;
|
||||
is_merged = 1;
|
||||
}
|
||||
}
|
||||
if (is_merged == 0) {
|
||||
or = q->re - p->rb; // overlap length on the reference
|
||||
oq = q->qb < p->qb? q->qe - p->qb : p->qe - q->qb; // overlap length on the query
|
||||
mr = q->re - q->rb < p->re - p->rb? q->re - q->rb : p->re - p->rb; // min ref len in alignment
|
||||
mq = q->qe - q->qb < p->qe - p->qb? q->qe - q->qb : p->qe - p->qb; // min qry len in alignment
|
||||
if (or > mask_level_redun * mr && oq > mask_level_redun * mq) { // one of the hits is redundant
|
||||
if (p->score < q->score) {
|
||||
p->qe = p->qb;
|
||||
break;
|
||||
} else q->qe = q->qb;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -401,6 +421,11 @@ int mem_sort_and_dedup(int n, mem_alnreg_t *a, float mask_level_redun)
|
|||
return m;
|
||||
}
|
||||
|
||||
int mem_sort_and_dedup(int n, mem_alnreg_t *a, float mask_level_redun)
|
||||
{
|
||||
return mem_sort_and_dedup2(n, a, mask_level_redun, -1);
|
||||
}
|
||||
|
||||
int mem_test_and_remove_exact(const mem_opt_t *opt, int n, mem_alnreg_t *a, int qlen)
|
||||
{
|
||||
if (!(opt->flag & MEM_F_SELF_OVLP) || n == 0 || a->truesc != qlen * opt->a) return n;
|
||||
|
|
@ -960,7 +985,8 @@ mem_alnreg_v mem_align1_core(const mem_opt_t *opt, const bwt_t *bwt, const bntse
|
|||
free(chn.a[i].seeds);
|
||||
}
|
||||
free(chn.a);
|
||||
regs.n = mem_sort_and_dedup(regs.n, regs.a, opt->mask_level_redun);
|
||||
if (opt->flag & MEM_F_MERGE_REG) regs.n = mem_sort_and_dedup2(regs.n, regs.a, opt->mask_level, opt->w);
|
||||
else regs.n = mem_sort_and_dedup(regs.n, regs.a, opt->mask_level_redun);
|
||||
if (opt->flag & MEM_F_SELF_OVLP)
|
||||
regs.n = mem_test_and_remove_exact(opt, regs.n, regs.a, l_seq);
|
||||
if (bwa_verbose >= 4) {
|
||||
|
|
|
|||
1
bwamem.h
1
bwamem.h
|
|
@ -18,6 +18,7 @@ typedef struct __smem_i smem_i;
|
|||
#define MEM_F_NO_RESCUE 0x20
|
||||
#define MEM_F_SELF_OVLP 0x40
|
||||
#define MEM_F_ALN_REG 0x80
|
||||
#define MEM_F_MERGE_REG 0x100
|
||||
|
||||
typedef struct {
|
||||
int a, b; // match score and mismatch penalty
|
||||
|
|
|
|||
|
|
@ -53,7 +53,7 @@ int main_mem(int argc, char *argv[])
|
|||
|
||||
opt = mem_opt_init();
|
||||
memset(&opt0, 0, sizeof(mem_opt_t));
|
||||
while ((c = getopt(argc, argv, "epaFMCSPHk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:")) >= 0) {
|
||||
while ((c = getopt(argc, argv, "epaFMCSPHVk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:")) >= 0) {
|
||||
if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
|
||||
else if (c == 'x') mode = optarg;
|
||||
else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1;
|
||||
|
|
@ -69,6 +69,7 @@ int main_mem(int argc, char *argv[])
|
|||
else if (c == 'S') opt->flag |= MEM_F_NO_RESCUE;
|
||||
else if (c == 'e') opt->flag |= MEM_F_SELF_OVLP;
|
||||
else if (c == 'F') opt->flag |= MEM_F_ALN_REG;
|
||||
else if (c == 'V') opt->flag |= MEM_F_MERGE_REG;
|
||||
else if (c == 'c') opt->max_occ = atoi(optarg), opt0.max_occ = 1;
|
||||
else if (c == 'd') opt->zdrop = atoi(optarg), opt0.zdrop = 1;
|
||||
else if (c == 'v') bwa_verbose = atoi(optarg);
|
||||
|
|
@ -147,7 +148,7 @@ int main_mem(int argc, char *argv[])
|
|||
fprintf(stderr, " -U INT penalty for an unpaired read pair [%d]\n", opt->pen_unpaired);
|
||||
fprintf(stderr, " -x STR read type. Setting -x changes multiple parameters unless overriden [null]\n");
|
||||
fprintf(stderr, " pacbio: -k17 -W40 -w200 -c1000 -r10 -A2 -B5 -O2 -E1 -L0\n");
|
||||
fprintf(stderr, " pbread: -k13 -W40 -w200 -c1000 -r10 -A2 -B5 -O2 -E1 -N25 -FeaD.001\n");
|
||||
fprintf(stderr, " pbread: -k13 -W40 -w200 -c1000 -r10 -A2 -B5 -O2 -E1 -N25 -FVeaD.001\n");
|
||||
fprintf(stderr, "\nInput/output options:\n\n");
|
||||
fprintf(stderr, " -p first query file consists of interleaved paired-end sequences\n");
|
||||
fprintf(stderr, " -R STR read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n");
|
||||
|
|
@ -182,11 +183,12 @@ int main_mem(int argc, char *argv[])
|
|||
if (opt0.split_factor == 0.) opt->split_factor = 10.;
|
||||
if (!opt0.min_chain_weight) opt->min_chain_weight = 40;
|
||||
if (strcmp(mode, "pbread1") == 0 || strcmp(mode, "pbread") == 0) {
|
||||
opt->flag |= MEM_F_ALL | MEM_F_SELF_OVLP | MEM_F_ALN_REG;
|
||||
opt->flag |= MEM_F_ALL | MEM_F_SELF_OVLP | MEM_F_ALN_REG | MEM_F_MERGE_REG;
|
||||
if (!opt0.min_seed_len) opt->min_seed_len = 13;
|
||||
if (!opt0.max_chain_extend) opt->max_chain_extend = 25;
|
||||
if (opt0.drop_ratio == 0.) opt->drop_ratio = .001;
|
||||
} else {
|
||||
opt->flag |= MEM_F_MERGE_REG;
|
||||
if (!opt0.min_seed_len) opt->min_seed_len = 17;
|
||||
if (!opt0.pen_clip5) opt->pen_clip5 = 0;
|
||||
if (!opt0.pen_clip3) opt->pen_clip3 = 0;
|
||||
|
|
|
|||
Loading…
Reference in New Issue