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debugging code

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This commit is contained in:
Heng Li
2018-10-29 19:50:31 -04:00
parent e9dcd7b2bc
commit e39080fea6
2 changed files with 9 additions and 4 deletions
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9
index.c
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@@ -148,12 +148,13 @@ int mm_idx_getseq2(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, u
uint32_t i, z;
memset(b, 0, en - st);
z = mm_idx_bed_query(mi, (uint64_t)rid << 32 | st);
for (i = z + 1; i < mi->n_R; ++i) {
for (i = z < 0? 0 : z; i < mi->n_R; ++i) {
uint32_t j, rr, rs, re;
rr = mi->R[i].x >> 32, rs = (uint32_t)mi->R[i].x, re = mi->R[i].end;
if (rr != rid || rs >= en) break;
assert(rs >= st);
for (j = rs; j < re; ++j)
if (rr > rid || rs >= en) break;
if (rr < rid) continue;
re = re < en? re : en;
for (j = st > rs? st : rs; j < re; ++j)
b[j - st] = mi->R[i].score;
}
}

4
ksw2_extd2_sse.c
View File

@@ -112,6 +112,9 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
if (qd) {
int8_t *tmp = (int8_t*)dv;
for (t = 0; t < tlen; ++t) tmp[t] = -qd[t];
fprintf(stderr, "%d\t%d\t%x\n", tlen, qlen, flag&KSW_EZ_RIGHT);
for (t = 0; t < tlen; ++t) fputc("ACGTN"[target[t]], stderr); fputc('\n', stderr);
for (t = 0; t < tlen; ++t) fputc('0' + qd[t], stderr); fputc('\n', stderr);
}
if (!approx_max) {
H = (int32_t*)kmalloc(km, tlen_ * 16 * 4);
@@ -383,6 +386,7 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
last_st = st, last_en = en;
//for (t = st0; t <= en0; ++t) printf("(%d,%d)\t(%d,%d,%d,%d)\t%d\n", r, t, ((int8_t*)u)[t], ((int8_t*)v)[t], ((int8_t*)x)[t], ((int8_t*)y)[t], H[t]); // for debugging
}
fprintf(stderr, "score: %d\n", ez->score);
kfree(km, mem);
if (!approx_max) kfree(km, H);
if (with_cigar) { // backtrack