From 00a07f61bf3b62817ba4d1200c4fca0dab60417d Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 15 Apr 2014 16:16:04 -0400 Subject: [PATCH] r721: merge overlapping hits by default --- bwamem.c | 10 ++-------- bwamem.h | 1 - bwamem_pair.c | 4 ++-- fastmap.c | 8 +++----- main.c | 2 +- 5 files changed, 8 insertions(+), 17 deletions(-) diff --git a/bwamem.c b/bwamem.c index 2f22b68c..3f1694c0 100644 --- a/bwamem.c +++ b/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_dedup2(int n, mem_alnreg_t *a, float mask_level_redun, int merge_bw) +int mem_sort_and_dedup(int n, mem_alnreg_t *a, float mask_level_redun, int merge_bw) { int m, i, j; if (n <= 1) return n; @@ -420,11 +420,6 @@ int mem_sort_and_dedup2(int n, mem_alnreg_t *a, float mask_level_redun, int merg 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; @@ -984,8 +979,7 @@ 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); - if (opt->flag & MEM_F_MERGE_REG) regs.n = mem_sort_and_dedup2(regs.n, regs.a, opt->mask_level_redun, opt->w); - else regs.n = mem_sort_and_dedup(regs.n, regs.a, opt->mask_level_redun); + regs.n = mem_sort_and_dedup(regs.n, regs.a, opt->mask_level_redun, opt->w); 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) { diff --git a/bwamem.h b/bwamem.h index 488d1cf0..53472fe2 100644 --- a/bwamem.h +++ b/bwamem.h @@ -18,7 +18,6 @@ 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 diff --git a/bwamem_pair.c b/bwamem_pair.c index bbd2cdba..0c4ea5e3 100644 --- a/bwamem_pair.c +++ b/bwamem_pair.c @@ -109,7 +109,7 @@ void mem_pestat(const mem_opt_t *opt, int64_t l_pac, int n, const mem_alnreg_v * 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) { - extern int mem_sort_and_dedup(int n, mem_alnreg_t *a, float mask_level_redun); + extern int mem_sort_and_dedup(int n, mem_alnreg_t *a, float mask_level_redun, int merge_bw); int64_t l_pac = bns->l_pac; int i, r, skip[4], n = 0, rid; for (r = 0; r < 4; ++r) @@ -170,7 +170,7 @@ int mem_matesw(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co } ++n; } - if (n) ma->n = mem_sort_and_dedup(ma->n, ma->a, opt->mask_level_redun); + if (n) ma->n = mem_sort_and_dedup(ma->n, ma->a, opt->mask_level_redun, -1); if (rev) free(rev); free(ref); } diff --git a/fastmap.c b/fastmap.c index b898adb9..81c0f207 100644 --- a/fastmap.c +++ b/fastmap.c @@ -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, "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) { + 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) { 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; @@ -69,7 +69,6 @@ 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); @@ -148,7 +147,7 @@ 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 -FVeaD.001\n"); + fprintf(stderr, " pbread: -k13 -W40 -w200 -c1000 -r10 -A2 -B5 -O2 -E1 -N25 -FeaD.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"); @@ -183,12 +182,11 @@ 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 | MEM_F_MERGE_REG; + opt->flag |= MEM_F_ALL | MEM_F_SELF_OVLP | MEM_F_ALN_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; diff --git a/main.c b/main.c index 17318a90..661f6149 100644 --- a/main.c +++ b/main.c @@ -4,7 +4,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.8-r720-dirty" +#define PACKAGE_VERSION "0.7.8-r721-dirty" #endif int bwa_fa2pac(int argc, char *argv[]);