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fixed a bug in ksw2

This commit is contained in:
Heng Li 2017-06-25 10:22:13 -04:00
parent ef5dd318ca
commit 72dfb0c99e
3 changed files with 6 additions and 2 deletions
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2
align.c
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@ -180,6 +180,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
qseq = &qseq0[rev][qs];
mm_idx_getseq(mi, rid, rs, re, tseq);
#if 0
int k;
fprintf(stderr, "===> [%d] %d-%d %c (%s:%d-%d) <===\n", i, qs, qe, "+-"[rev], mi->seq[rid].name, rs, re);
for (k = 0; k < re - rs; ++k) fputc("ACGTN"[tseq[k]], stderr); fputc('\n', stderr);
for (k = 0; k < qe - qs; ++k) fputc("ACGTN"[qseq[k]], stderr); fputc('\n', stderr);
@ -189,6 +190,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar);
if (ez->score == KSW_NEG_INF) { // truncated by Z-drop
int j;
abort();
for (j = i - 1; j >= 0; --j)
if ((int32_t)a[r->as + j].x < re + ez->max_t)
break;

2
ksw2_extz2_sse.c
View File

@ -53,7 +53,7 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
m1_ = _mm_set1_epi8(m - 1); // wildcard
ez->max_q = ez->max_t = ez->mqe_t = ez->mte_q = -1;
ez->max = 0, ez->mqe = ez->mte = KSW_NEG_INF;
ez->max = 0, ez->score = ez->mqe = ez->mte = KSW_NEG_INF;
ez->n_cigar = 0;
wl = wr = w;

4
main.c
View File

@ -54,7 +54,7 @@ int main(int argc, char *argv[])
mm_realtime0 = realtime();
mm_mapopt_init(&opt);
while ((c = getopt(argc, argv, "w:k:B:b:t:r:f:Vv:Ng:I:d:ST:s:Dx:Hp:m:")) >= 0) {
while ((c = getopt(argc, argv, "w:k:B:b:t:r:f:Vv:Ng:I:d:ST:s:Dx:Hp:m:z:")) >= 0) {
if (c == 'w') w = atoi(optarg);
else if (c == 'k') k = atoi(optarg);
else if (c == 'b') b = atoi(optarg);
@ -72,6 +72,7 @@ int main(int argc, char *argv[])
else if (c == 'S') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
else if (c == 'T') opt.sdust_thres = atoi(optarg);
else if (c == 's') opt.min_score = atoi(optarg);
else if (c == 'z') opt.zdrop = atoi(optarg);
else if (c == 'V') {
puts(MM_VERSION);
return 0;
@ -113,6 +114,7 @@ int main(int argc, char *argv[])
// fprintf(stderr, " -D skip self mappings but keep dual mappings\n"); // too confusing to expose to end users
fprintf(stderr, " -S skip self and dual mappings\n");
fprintf(stderr, " -p FLOAT threshold to output a mapping [%g]\n", opt.pri_ratio);
fprintf(stderr, " -z INT Z-drop score [%d]\n", opt.zdrop);
fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n");
fprintf(stderr, " ava10k: -Sw5 -L100 -m0 (PacBio/ONT all-vs-all read mapping)\n");
fprintf(stderr, " Input/Output:\n");