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Merge branch 'master' into sr

This commit is contained in:
Heng Li 2017-09-20 11:15:14 -04:00
parent 7a9b4db874 75e6bbc9f6
commit 645db3350e
4 changed files with 14 additions and 21 deletions
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13
align.c
View File

@ -65,7 +65,7 @@ static int mm_check_zdrop(const uint8_t *qseq, const uint8_t *tseq, uint32_t n_c
static void mm_update_extra(mm_extra_t *p, const uint8_t *qseq, const uint8_t *tseq, const int8_t *mat, int8_t q, int8_t e)
{
uint32_t k, l, toff = 0, qoff = 0;
int32_t s = 0, max = 0, n_gtag = 0, n_ctac = 0;
int32_t s = 0, max = 0;
if (p == 0) return;
for (k = 0; k < p->n_cigar; ++k) {
uint32_t op = p->cigar[k]&0xf, len = p->cigar[k]>>4;
@ -99,14 +99,10 @@ static void mm_update_extra(mm_extra_t *p, const uint8_t *qseq, const uint8_t *t
uint8_t b[4];
b[0] = tseq[toff], b[1] = tseq[toff+1];
b[2] = tseq[toff+len-2], b[3] = tseq[toff+len-1];
if (memcmp(b, "\2\3\0\2", 4) == 0) ++n_gtag;
else if (memcmp(b, "\1\3\0\1", 4) == 0) ++n_ctac;
toff += len, p->blen += len;
}
}
p->dp_max = max;
if (n_gtag > n_ctac) p->trans_strand = 1;
else if (n_gtag < n_ctac) p->trans_strand = 2;
}
static void mm_append_cigar(mm_reg1_t *r, uint32_t n_cigar, uint32_t *cigar) // TODO: this calls the libc realloc()
@ -284,7 +280,6 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
if (opt->flag & MM_F_SPLICE) {
if (splice_flag & MM_F_SPLICE_FOR) extra_flag |= rev? KSW_EZ_SPLICE_REV : KSW_EZ_SPLICE_FOR;
if (splice_flag & MM_F_SPLICE_REV) extra_flag |= rev? KSW_EZ_SPLICE_FOR : KSW_EZ_SPLICE_REV;
if (splice_flag & MM_F_SPLICE_BOTH) extra_flag |= KSW_EZ_SPLICE_FOR|KSW_EZ_SPLICE_REV;
}
// compute rs0 and qs0
@ -468,7 +463,7 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
memset(&ez, 0, sizeof(ksw_extz_t));
for (i = 0; i < n_regs; ++i) {
mm_reg1_t r2;
if ((opt->flag&MM_F_SPLICE) && (opt->flag&MM_F_SPLICE_FOR) && (opt->flag&MM_F_SPLICE_REV)) {
if ((opt->flag&MM_F_SPLICE) && (opt->flag&MM_F_SPLICE_FOR) && (opt->flag&MM_F_SPLICE_REV)) { // then do two rounds of alignments for both strands
mm_reg1_t s[2], s2[2];
int which, trans_strand;
s[0] = s[1] = regs[i];
@ -485,9 +480,9 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
free(s[0].p);
}
regs[i].p->trans_strand = trans_strand;
} else {
} else { // one round of alignment
mm_align1(km, opt, mi, qlen, qseq0, &regs[i], &r2, a, &ez, opt->flag);
if ((opt->flag&MM_F_SPLICE) && !(opt->flag&MM_F_SPLICE_BOTH))
if (opt->flag&MM_F_SPLICE)
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);

11
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r414-dirty"
#define MM_VERSION "2.2-r421-dirty"
#ifdef __linux__
#include <sys/resource.h>
@ -124,11 +124,10 @@ int main(int argc, char *argv[])
if (x < 1.0) opt.mid_occ_frac = x, opt.mid_occ = 0;
else opt.mid_occ = (int)(x + .499);
} else if (c == 'u') {
if (*optarg == 'b') opt.flag |= MM_F_SPLICE_FOR|MM_F_SPLICE_REV;
else if (*optarg == 'B') opt.flag |= MM_F_SPLICE_BOTH;
else if (*optarg == 'f') opt.flag |= MM_F_SPLICE_FOR, opt.flag &= ~MM_F_SPLICE_REV;
else if (*optarg == 'r') opt.flag |= MM_F_SPLICE_REV, opt.flag &= ~MM_F_SPLICE_FOR;
else if (*optarg == 'n') opt.flag &= ~(MM_F_SPLICE_FOR|MM_F_SPLICE_REV);
if (*optarg == 'b') opt.flag |= MM_F_SPLICE_FOR|MM_F_SPLICE_REV; // both strands
else if (*optarg == 'f') opt.flag |= MM_F_SPLICE_FOR, opt.flag &= ~MM_F_SPLICE_REV; // match GT-AG
else if (*optarg == 'r') opt.flag |= MM_F_SPLICE_REV, opt.flag &= ~MM_F_SPLICE_FOR; // match CT-AC (reverse complement of GT-AG)
else if (*optarg == 'n') opt.flag &= ~(MM_F_SPLICE_FOR|MM_F_SPLICE_REV); // don't try to match the GT-AG signal
else {
fprintf(stderr, "[E::%s] unrecognized cDNA direction\n", __func__);
return 1;

4
map.c
View File

@ -38,8 +38,8 @@ void mm_mapopt_init(mm_mapopt_t *opt)
void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
{
if (opt->flag & MM_F_SPLICE_BOTH)
opt->flag &= ~(MM_F_SPLICE_FOR|MM_F_SPLICE_REV);
if ((opt->flag & MM_F_SPLICE_FOR) && (opt->flag & MM_F_SPLICE_REV))
opt->flag |= MM_F_SPLICE;
if (opt->mid_occ <= 0)
opt->mid_occ = mm_idx_cal_max_occ(mi, opt->mid_occ_frac);
if (mm_verbose >= 3)

7
minimap.h
View File

@ -12,10 +12,9 @@
#define MM_F_NO_QUAL 0x010
#define MM_F_OUT_CG 0x020
#define MM_F_OUT_CS 0x040
#define MM_F_SPLICE 0x080
#define MM_F_SPLICE_FOR 0x100
#define MM_F_SPLICE_REV 0x200
#define MM_F_SPLICE_BOTH 0x400
#define MM_F_SPLICE 0x080 // splice mode
#define MM_F_SPLICE_FOR 0x100 // match GT-AG
#define MM_F_SPLICE_REV 0x200 // match CT-AC, the reverse complement of GT-AG
#define MM_F_NO_SAM_SQ 0x800
#define MM_F_SR 0x1000