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optionally write XB to include alignment score 

request from 4DN-DCIC
This commit is contained in:
Heng Li 2018-04-02 10:43:41 -04:00
parent a9c688ac92
commit eb7dbc1429
4 changed files with 11 additions and 2 deletions
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5
bwamem.c
View File

@ -932,7 +932,10 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
if (p->alt_sc > 0) if (p->alt_sc > 0)
ksprintf(str, "\tpa:f:%.3f", (double)p->score / p->alt_sc); ksprintf(str, "\tpa:f:%.3f", (double)p->score / p->alt_sc);
} }
if (p->XA) { kputsn("\tXA:Z:", 6, str); kputs(p->XA, str); } if (p->XA) {
kputsn((opt->flag&MEM_F_XB)? "\tXB:Z:" : "\tXA:Z:", 6, str);
kputs(p->XA, str);
}
if (s->comment) { kputc('\t', str); kputs(s->comment, str); } if (s->comment) { kputc('\t', str); kputs(s->comment, str); }
if ((opt->flag&MEM_F_REF_HDR) && p->rid >= 0 && bns->anns[p->rid].anno != 0 && bns->anns[p->rid].anno[0] != 0) { if ((opt->flag&MEM_F_REF_HDR) && p->rid >= 0 && bns->anns[p->rid].anno != 0 && bns->anns[p->rid].anno[0] != 0) {
int tmp; int tmp;

1
bwamem.h
View File

@ -20,6 +20,7 @@ typedef struct __smem_i smem_i;
#define MEM_F_SOFTCLIP 0x200 #define MEM_F_SOFTCLIP 0x200
#define MEM_F_SMARTPE 0x400 #define MEM_F_SMARTPE 0x400
#define MEM_F_PRIMARY5 0x800 #define MEM_F_PRIMARY5 0x800
#define MEM_F_XB 0x1000
typedef struct { typedef struct {
int a, b; // match score and mismatch penalty int a, b; // match score and mismatch penalty

4
bwamem_extra.c
View File

@ -126,6 +126,10 @@ char **mem_gen_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac
kputc("MIDSHN"[t.cigar[k]&0xf], &str); kputc("MIDSHN"[t.cigar[k]&0xf], &str);
} }
kputc(',', &str); kputw(t.NM, &str); kputc(',', &str); kputw(t.NM, &str);
if (opt->flag & MEM_F_XB) {
kputc(',', &str);
kputw(t.score, &str);
}
kputc(';', &str); kputc(';', &str);
free(t.cigar); free(t.cigar);
kputsn(str.s, str.l, &aln[r]); kputsn(str.s, str.l, &aln[r]);

3
fastmap.c
View File

@ -130,7 +130,7 @@ int main_mem(int argc, char *argv[])
aux.opt = opt = mem_opt_init(); aux.opt = opt = mem_opt_init();
memset(&opt0, 0, sizeof(mem_opt_t)); memset(&opt0, 0, sizeof(mem_opt_t));
while ((c = getopt(argc, argv, "51paMCSPVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:o:f:W:x:G:h:y:K:X:H:")) >= 0) { while ((c = getopt(argc, argv, "51paMCSPVYjuk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:o:f:W:x:G:h:y:K:X:H:")) >= 0) {
if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1; if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
else if (c == '1') no_mt_io = 1; else if (c == '1') no_mt_io = 1;
else if (c == 'x') mode = optarg; else if (c == 'x') mode = optarg;
@ -148,6 +148,7 @@ int main_mem(int argc, char *argv[])
else if (c == 'Y') opt->flag |= MEM_F_SOFTCLIP; else if (c == 'Y') opt->flag |= MEM_F_SOFTCLIP;
else if (c == 'V') opt->flag |= MEM_F_REF_HDR; else if (c == 'V') opt->flag |= MEM_F_REF_HDR;
else if (c == '5') opt->flag |= MEM_F_PRIMARY5; else if (c == '5') opt->flag |= MEM_F_PRIMARY5;
else if (c == 'u') opt->flag |= MEM_F_XB;
else if (c == 'c') opt->max_occ = atoi(optarg), opt0.max_occ = 1; 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 == 'd') opt->zdrop = atoi(optarg), opt0.zdrop = 1;
else if (c == 'v') bwa_verbose = atoi(optarg); else if (c == 'v') bwa_verbose = atoi(optarg);