INNER CODE UNIT · C
qseq
lh3/ksw2 · cli.c:60
qseq = (uint8_t*)calloc(qlen + 33, 1); // 32 for gaba
tseq = (uint8_t*)calloc(tlen + 33, 1);
for (i = 0; i < qlen; ++i)
qseq[i] = seq_nt4_table[(uint8_t)qseq_[i]];
for (i = 0; i < tlen; ++i)
tseq[i] = seq_nt4_table[(uint8_t)tseq_[i]];
if (strcmp(algo, "gg") == 0) {
if (flag & KSW_EZ_SCORE_ONLY) ez->score = ksw_gg(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, w, 0, 0, 0);
else ez->score = ksw_gg(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, w, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
} else if (strcmp(algo, "gg2") == 0) {
if (flag & KSW_EZ_SCORE_ONLY) ez->score = ksw_gg2(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, w, 0, 0, 0);
else ez->score = ksw_gg2(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, w, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
}
else if (strcmp(algo, "gg2_sse") == 0) ez->score = ksw_gg2_sse(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, w, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
else if (strcmp(algo, "extz") == 0) ksw_extz(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, w, zdrop, flag, ez);
else if (strcmp(algo, "extz2_sse") == 0) ksw_extz2_sse(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, w, zdrop, 0, flag, ez);
else if (strcmp(algo, "extd") == 0) ksw_extd(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, q2, e2, w, zdrop, flag, ez);
else if (strcmp(algo, "extd2_sse") == 0) ksw_extd2_sse(km, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, q, e, q2, e2, w, zdrop, 0, flag, ez);