r721: merge overlapping hits by default
This commit is contained in:
Heng Li
parent
45f24b4ae8
commit
00a07f61bf
10
bwamem.c
10
bwamem.c
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@ -358,7 +358,7 @@ KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt)
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#define alnreg_hlt(a, b) ((a).score > (b).score || ((a).score == (b).score && (a).hash < (b).hash))
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KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt)
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int mem_sort_and_dedup2(int n, mem_alnreg_t *a, float mask_level_redun, int merge_bw)
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int mem_sort_and_dedup(int n, mem_alnreg_t *a, float mask_level_redun, int merge_bw)
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{
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int m, i, j;
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if (n <= 1) return n;
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@ -420,11 +420,6 @@ int mem_sort_and_dedup2(int n, mem_alnreg_t *a, float mask_level_redun, int merg
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return m;
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}
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int mem_sort_and_dedup(int n, mem_alnreg_t *a, float mask_level_redun)
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{
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return mem_sort_and_dedup2(n, a, mask_level_redun, -1);
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}
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int mem_test_and_remove_exact(const mem_opt_t *opt, int n, mem_alnreg_t *a, int qlen)
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{
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if (!(opt->flag & MEM_F_SELF_OVLP) || n == 0 || a->truesc != qlen * opt->a) return n;
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@ -984,8 +979,7 @@ mem_alnreg_v mem_align1_core(const mem_opt_t *opt, const bwt_t *bwt, const bntse
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free(chn.a[i].seeds);
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}
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free(chn.a);
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if (opt->flag & MEM_F_MERGE_REG) regs.n = mem_sort_and_dedup2(regs.n, regs.a, opt->mask_level_redun, opt->w);
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else regs.n = mem_sort_and_dedup(regs.n, regs.a, opt->mask_level_redun);
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regs.n = mem_sort_and_dedup(regs.n, regs.a, opt->mask_level_redun, opt->w);
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if (opt->flag & MEM_F_SELF_OVLP)
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regs.n = mem_test_and_remove_exact(opt, regs.n, regs.a, l_seq);
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if (bwa_verbose >= 4) {
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1
bwamem.h
1
bwamem.h
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@ -18,7 +18,6 @@ typedef struct __smem_i smem_i;
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#define MEM_F_NO_RESCUE 0x20
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#define MEM_F_SELF_OVLP 0x40
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#define MEM_F_ALN_REG 0x80
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#define MEM_F_MERGE_REG 0x100
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typedef struct {
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int a, b; // match score and mismatch penalty
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@ -109,7 +109,7 @@ void mem_pestat(const mem_opt_t *opt, int64_t l_pac, int n, const mem_alnreg_v *
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int mem_matesw(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], const mem_alnreg_t *a, int l_ms, const uint8_t *ms, mem_alnreg_v *ma)
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{
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extern int mem_sort_and_dedup(int n, mem_alnreg_t *a, float mask_level_redun);
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extern int mem_sort_and_dedup(int n, mem_alnreg_t *a, float mask_level_redun, int merge_bw);
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int64_t l_pac = bns->l_pac;
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int i, r, skip[4], n = 0, rid;
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for (r = 0; r < 4; ++r)
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@ -170,7 +170,7 @@ int mem_matesw(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
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}
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++n;
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}
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if (n) ma->n = mem_sort_and_dedup(ma->n, ma->a, opt->mask_level_redun);
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if (n) ma->n = mem_sort_and_dedup(ma->n, ma->a, opt->mask_level_redun, -1);
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if (rev) free(rev);
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free(ref);
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}
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@ -53,7 +53,7 @@ int main_mem(int argc, char *argv[])
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opt = mem_opt_init();
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memset(&opt0, 0, sizeof(mem_opt_t));
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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) {
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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) {
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if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
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else if (c == 'x') mode = optarg;
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else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1;
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@ -69,7 +69,6 @@ int main_mem(int argc, char *argv[])
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else if (c == 'S') opt->flag |= MEM_F_NO_RESCUE;
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else if (c == 'e') opt->flag |= MEM_F_SELF_OVLP;
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else if (c == 'F') opt->flag |= MEM_F_ALN_REG;
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else if (c == 'V') opt->flag |= MEM_F_MERGE_REG;
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else if (c == 'c') opt->max_occ = atoi(optarg), opt0.max_occ = 1;
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else if (c == 'd') opt->zdrop = atoi(optarg), opt0.zdrop = 1;
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else if (c == 'v') bwa_verbose = atoi(optarg);
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@ -148,7 +147,7 @@ int main_mem(int argc, char *argv[])
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fprintf(stderr, " -U INT penalty for an unpaired read pair [%d]\n", opt->pen_unpaired);
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fprintf(stderr, " -x STR read type. Setting -x changes multiple parameters unless overriden [null]\n");
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fprintf(stderr, " pacbio: -k17 -W40 -w200 -c1000 -r10 -A2 -B5 -O2 -E1 -L0\n");
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fprintf(stderr, " pbread: -k13 -W40 -w200 -c1000 -r10 -A2 -B5 -O2 -E1 -N25 -FVeaD.001\n");
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fprintf(stderr, " pbread: -k13 -W40 -w200 -c1000 -r10 -A2 -B5 -O2 -E1 -N25 -FeaD.001\n");
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fprintf(stderr, "\nInput/output options:\n\n");
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fprintf(stderr, " -p first query file consists of interleaved paired-end sequences\n");
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fprintf(stderr, " -R STR read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n");
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@ -183,12 +182,11 @@ int main_mem(int argc, char *argv[])
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if (opt0.split_factor == 0.) opt->split_factor = 10.;
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if (!opt0.min_chain_weight) opt->min_chain_weight = 40;
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if (strcmp(mode, "pbread1") == 0 || strcmp(mode, "pbread") == 0) {
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opt->flag |= MEM_F_ALL | MEM_F_SELF_OVLP | MEM_F_ALN_REG | MEM_F_MERGE_REG;
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opt->flag |= MEM_F_ALL | MEM_F_SELF_OVLP | MEM_F_ALN_REG;
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if (!opt0.min_seed_len) opt->min_seed_len = 13;
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if (!opt0.max_chain_extend) opt->max_chain_extend = 25;
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if (opt0.drop_ratio == 0.) opt->drop_ratio = .001;
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} else {
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opt->flag |= MEM_F_MERGE_REG;
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if (!opt0.min_seed_len) opt->min_seed_len = 17;
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if (!opt0.pen_clip5) opt->pen_clip5 = 0;
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if (!opt0.pen_clip3) opt->pen_clip3 = 0;
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