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r611: document --idx-no-seq; better inv aln

This commit is contained in:
Heng Li 2017-12-08 13:16:18 -05:00
parent 98a999fe44
commit 0e42628ef6
3 changed files with 14 additions and 3 deletions
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1
align.c
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@ -582,6 +582,7 @@ static int mm_align1_inv(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, i
r_inv->inv = 1;
r_inv->rev = !r1->rev;
r_inv->rid = r1->rid;
r_inv->div = -1.0f;
r_inv->qs = r1->qe + q_off, r_inv->qe = r_inv->qs + ez->max_q + 1;
r_inv->rs = r1->re + t_off, r_inv->re = r_inv->rs + ez->max_t + 1;
mm_update_extra(r_inv, &qseq[q_off], qual? &qual[q_off] : 0, &tseq[t_off], mat, opt->q, opt->e);

4
format.c
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@ -202,7 +202,9 @@ static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_
static inline void write_tags(kstring_t *s, const mm_reg1_t *r)
{
int type = r->inv? 'I' : r->id == r->parent? 'P' : 'S';
int type;
if (r->id == r->parent) type = r->inv? 'I' : 'P';
else type = r->inv? 'i' : 'S';
if (r->p) {
mm_sprintf_lite(s, "\tNM:i:%d\tms:i:%d\tAS:i:%d\tnn:i:%d", r->blen - r->mlen + r->p->n_ambi, r->p->dp_max, r->p->dp_score, r->p->n_ambi);
if (r->p->trans_strand == 1 || r->p->trans_strand == 2)

12
minimap2.1
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@ -1,4 +1,4 @@
.TH minimap2 1 "11 November 2017" "minimap2-2.5 (r572)" "Bioinformatics tools"
.TH minimap2 1 "8 December 2017" "minimap2-2.5-dirty (r611)" "Bioinformatics tools"
.SH NAME
.PP
minimap2 - mapping and alignment between collections of DNA sequences
@ -99,6 +99,14 @@ multiple times to map it against each batch of target sequences.
may be ending with k/K/m/M/g/G. NB: mapping quality is incorrect given a
multi-part index.
.TP
.B --idx-no-seq
Don't store target sequences in the index. It saves disk space and memory but
the index generated with this option will not work with
.B -a
or
.BR -c .
When base-level alignment is not requested, this option is automatically applied.
.TP
.BI -d \ FILE
Save the minimizer index of
.I target.fa
@ -461,7 +469,7 @@ cb | cb | cb
r | c | l .
Tag Type Description
_
tp A Type of aln: P/primary, S/secondary and I/inversion
tp A Type of aln: P/primary, S/secondary and I,i/inversion
cm i Number of minimizers on the chain
s1 i Chaining score
s2 i Chaining score of the best secondary chain