From 1739a260fb044eded97b3271cd5204c79363fa76 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 5 Feb 2019 14:19:17 -0500 Subject: [PATCH] r913: output tag "rl", length of unseedable regs --- format.c | 17 +++++++++++++++-- main.c | 2 +- map.c | 8 ++++---- minimap2.1 | 3 ++- mmpriv.h | 2 ++ 5 files changed, 24 insertions(+), 8 deletions(-) diff --git a/format.c b/format.c index e300fe7..2379a00 100644 --- a/format.c +++ b/format.c @@ -301,11 +301,12 @@ static inline void write_tags(kstring_t *s, const mm_reg1_t *r) if (r->split) mm_sprintf_lite(s, "\tzd:i:%d", r->split); } -void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag) +void mm_write_paf3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag, int rep_len) { s->l = 0; if (r == 0) { mm_sprintf_lite(s, "%s\t%d", t->name, t->l_seq); + if (rep_len >= 0) mm_sprintf_lite(s, "\trl:i:%d", rep_len); return; } mm_sprintf_lite(s, "%s\t%d\t%d\t%d\t%c\t", t->name, t->l_seq, r->qs, r->qe, "+-"[r->rev]); @@ -315,6 +316,7 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m mm_sprintf_lite(s, "\t%d\t%d", r->mlen, r->blen); mm_sprintf_lite(s, "\t%d", r->mapq); write_tags(s, r); + if (rep_len >= 0) mm_sprintf_lite(s, "\trl:i:%d", rep_len); if (r->p && (opt_flag & MM_F_OUT_CG)) { uint32_t k; mm_sprintf_lite(s, "\tcg:Z:"); @@ -327,6 +329,11 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m mm_sprintf_lite(s, "\t%s", t->comment); } +void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag) +{ + mm_write_paf3(s, mi, t, r, km, opt_flag, -1); +} + static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp) { extern unsigned char seq_comp_table[256]; @@ -377,7 +384,7 @@ static void write_sam_cigar(kstring_t *s, int sam_flag, int in_tag, int qlen, co } } -void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int seg_idx, int reg_idx, int n_seg, const int *n_regss, const mm_reg1_t *const* regss, void *km, int opt_flag) +void mm_write_sam3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int seg_idx, int reg_idx, int n_seg, const int *n_regss, const mm_reg1_t *const* regss, void *km, int opt_flag, int rep_len) { const int max_bam_cigar_op = 65535; int flag, n_regs = n_regss[seg_idx], cigar_in_tag = 0; @@ -528,6 +535,7 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se if (cigar_in_tag) write_sam_cigar(s, flag, 1, t->l_seq, r, opt_flag); } + if (rep_len >= 0) mm_sprintf_lite(s, "\trl:i:%d", rep_len); if ((opt_flag & MM_F_COPY_COMMENT) && t->comment) mm_sprintf_lite(s, "\t%s", t->comment); @@ -535,6 +543,11 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se s->s[s->l] = 0; // we always have room for an extra byte (see str_enlarge) } +void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int seg_idx, int reg_idx, int n_seg, const int *n_regss, const mm_reg1_t *const* regss, void *km, int opt_flag) +{ + mm_write_sam3(s, mi, t, seg_idx, reg_idx, n_seg, n_regss, regss, km, opt_flag, -1); +} + void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs) { int i; diff --git a/main.c b/main.c index 69c45b8..798f6d7 100644 --- a/main.c +++ b/main.c @@ -6,7 +6,7 @@ #include "mmpriv.h" #include "ketopt.h" -#define MM_VERSION "2.15-r911-dirty" +#define MM_VERSION "2.15-r913-dirty" #ifdef __linux__ #include diff --git a/map.c b/map.c index 16fbe06..0f1bac2 100644 --- a/map.c +++ b/map.c @@ -584,16 +584,16 @@ static void *worker_pipeline(void *shared, int step, void *in) if ((p->opt->flag & MM_F_NO_PRINT_2ND) && r->id != r->parent) continue; if (p->opt->flag & MM_F_OUT_SAM) - mm_write_sam2(&p->str, mi, t, i - seg_st, j, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag); + mm_write_sam3(&p->str, mi, t, i - seg_st, j, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag, s->rep_len[i]); else - mm_write_paf(&p->str, mi, t, r, km, p->opt->flag); + mm_write_paf3(&p->str, mi, t, r, km, p->opt->flag, s->rep_len[i]); mm_err_puts(p->str.s); } } else if (p->opt->flag & (MM_F_OUT_SAM|MM_F_PAF_NO_HIT)) { // output an empty hit, if requested if (p->opt->flag & MM_F_OUT_SAM) - mm_write_sam2(&p->str, mi, t, i - seg_st, -1, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag); + mm_write_sam3(&p->str, mi, t, i - seg_st, -1, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag, s->rep_len[i]); else - mm_write_paf(&p->str, mi, t, 0, 0, p->opt->flag); + mm_write_paf3(&p->str, mi, t, 0, 0, p->opt->flag, s->rep_len[i]); mm_err_puts(p->str.s); } } diff --git a/minimap2.1 b/minimap2.1 index 45ff89c..016af5e 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -1,4 +1,4 @@ -.TH minimap2 1 "10 January 2019" "minimap2-2.15-dirty (r911)" "Bioinformatics tools" +.TH minimap2 1 "5 Feburary 2019" "minimap2-2.15-dirty (r913)" "Bioinformatics tools" .SH NAME .PP minimap2 - mapping and alignment between collections of DNA sequences @@ -617,6 +617,7 @@ cg Z CIGAR string (only in PAF) cs Z Difference string dv f Approximate per-base sequence divergence de f Gap-compressed per-base sequence divergence +rl i Length of query regions harboring repetitive seeds .TE .PP diff --git a/mmpriv.h b/mmpriv.h index 2688bca..a059701 100644 --- a/mmpriv.h +++ b/mmpriv.h @@ -61,8 +61,10 @@ void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, i void mm_write_sam_hdr(const mm_idx_t *mi, const char *rg, const char *ver, int argc, char *argv[]); void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag); +void mm_write_paf3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag, int rep_len); void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs); void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int seg_idx, int reg_idx, int n_seg, const int *n_regs, const mm_reg1_t *const* regs, void *km, int opt_flag); +void mm_write_sam3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int seg_idx, int reg_idx, int n_seg, const int *n_regss, const mm_reg1_t *const* regss, void *km, int opt_flag, int rep_len); void mm_idxopt_init(mm_idxopt_t *opt); const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n);