From 0e42628ef63e97eca95c4afce91777b43597d010 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 8 Dec 2017 13:16:18 -0500 Subject: [PATCH] r611: document --idx-no-seq; better inv aln --- align.c | 1 + format.c | 4 +++- minimap2.1 | 12 ++++++++++-- 3 files changed, 14 insertions(+), 3 deletions(-) diff --git a/align.c b/align.c index 4bcc439..7a8e206 100644 --- a/align.c +++ b/align.c @@ -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); diff --git a/format.c b/format.c index fb8924d..89a93b6 100644 --- a/format.c +++ b/format.c @@ -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) diff --git a/minimap2.1 b/minimap2.1 index 17e22a0..8696bed 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -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