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r287: refined CLI options and manpage

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Heng Li
2017-08-12 12:26:04 -04:00
parent 0f4c823b0c
commit d240318741
5 changed files with 61 additions and 26 deletions
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align.c
+4 -4
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@@ -135,7 +135,7 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
for (i = 0; i < tlen; ++i) fputc("ACGTN"[tseq[i]], stderr); fputc('\n', stderr);
for (i = 0; i < qlen; ++i) fputc("ACGTN"[qseq[i]], stderr); fputc('\n', stderr);
}
if (opt->flag & MM_F_CDNA)
if (opt->flag & MM_F_SPLICE)
ksw_extd2_noins_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, 0, -1, opt->zdrop, flag, ez);
else if (opt->q == opt->q2 && opt->e == opt->e2)
ksw_extz2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, w, opt->zdrop, flag, ez);
@@ -259,7 +259,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
bw = (int)(opt->bw * 1.5 + 1.);
r2->cnt = 0;
if (!(opt->flag & MM_F_CDNA))
if (!(opt->flag & MM_F_SPLICE))
mm_fix_bad_ends(r, a, opt->bw, &as1, &cnt1);
else as1 = r->as, cnt1 = r->cnt;
mm_filter_bad_seeds(km, as1, cnt1, a, 10, 40, opt->max_gap>>1, 10);
@@ -362,7 +362,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
assert(re1 - rs1 <= re0 - rs0);
if (r->p) {
mm_idx_getseq(mi, rid, rs1, re1, tseq);
mm_update_extra(r->p, &qseq0[r->rev][qs1], tseq, mat, opt->q, opt->e, (opt->flag&MM_F_CDNA)? opt->q2 : 0);
mm_update_extra(r->p, &qseq0[r->rev][qs1], tseq, mat, opt->q, opt->e, (opt->flag&MM_F_SPLICE)? opt->q2 : 0);
}
kfree(km, tseq);
@@ -403,7 +403,7 @@ static int mm_align1_inv(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, i
if (ez->n_cigar == 0) goto end_align1_inv; // should never be here
mm_append_cigar(r_inv, ez->n_cigar, ez->cigar);
r_inv->p->dp_score = ez->max;
mm_update_extra(r_inv->p, qseq + q_off, tseq + t_off, mat, opt->q, opt->e, (opt->flag&MM_F_CDNA)? opt->q2 : 0);
mm_update_extra(r_inv->p, qseq + q_off, tseq + t_off, mat, opt->q, opt->e, (opt->flag&MM_F_SPLICE)? opt->q2 : 0);
r_inv->id = -1;
r_inv->parent = MM_PARENT_UNSET;
r_inv->inv = 1;