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read score from BED

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This commit is contained in:
Heng Li
2018-10-29 15:07:48 -04:00
parent 121731ebde
commit e9dcd7b2bc
3 changed files with 13 additions and 7 deletions
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3
align.c
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@@ -292,7 +292,8 @@ static void mm_update_cigar_eqx(mm_reg1_t *r, const uint8_t *qseq, const uint8_t
r->p = p;
}
static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint8_t *qseq, int tlen, const uint8_t *tseq, const int8_t *ob, const int8_t *mat, int w, int end_bonus, int zdrop, int flag, ksw_extz_t *ez)
static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint8_t *qseq, int tlen, const uint8_t *tseq, const int8_t *ob, const int8_t *mat,
int w, int end_bonus, int zdrop, int flag, ksw_extz_t *ez)
{
if (mm_dbg_flag & MM_DBG_PRINT_ALN_SEQ) {
int i;

16
index.c
View File

@@ -154,7 +154,7 @@ int mm_idx_getseq2(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, u
if (rr != rid || rs >= en) break;
assert(rs >= st);
for (j = rs; j < re; ++j)
b[j - st] = 1;
b[j - st] = mi->R[i].score;
}
}
return en - st;
@@ -625,20 +625,24 @@ mm_idx_bed_t *mm_idx_bed_read_list(const mm_idx_t *mi, const char *fn, uint32_t
while (ks_getuntil(ks, KS_SEP_LINE, &str, 0) >= 0) {
mm_idx_bed_t t;
char *p, *q;
int i, id = -1, st = -1, en = -1;
int i, id = -1, st = -1, en = -1, sc = -1;
for (p = q = str.s, i = 0;; ++p) {
if (*p == 0 || isspace(*p)) {
int32_t c = *p;
*p = 0;
if (i == 0) {
if (i == 0) { // chr
id = mm_idx_name2id(mi, q);
if (id < 0) break; // unknown name; TODO: throw a warning
} else if (i == 1) {
} else if (i == 1) { // start
st = atoi(q);
if (st < 0) break;
} else if (i == 2) {
} else if (i == 2) { // end
en = atoi(q);
if (en < 0) break;
} else if (i == 3) { // name; do nothing
} else if (i == 4) { // BED score
sc = atoi(q);
assert(sc >= 0 && sc <= 127);
} else break;
if (c == 0) break;
++i, q = p + 1;
@@ -647,7 +651,7 @@ mm_idx_bed_t *mm_idx_bed_read_list(const mm_idx_t *mi, const char *fn, uint32_t
if (en < 0) en = st + 1;
if (st < 0 || st >= en) continue;
if (m == n) EXPAND(r, m);
t.x = (uint64_t)id << 32 | st, t.end = en, t.idx = -1;
t.x = (uint64_t)id << 32 | st, t.end = en, t.score = sc >= 0? sc : 0, t.idx = -1;
r[n++] = t;
}
ks_destroy(ks);

1
minimap.h
View File

@@ -62,6 +62,7 @@ typedef struct {
typedef struct {
uint64_t x;
int32_t end, idx;
int32_t score; // NB: wasting 4 bytes due to memory alignment
} mm_idx_bed_t;
typedef struct {