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An option to output SEQ field for secondary alignment #687

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merged 5 commits into from
Apr 21, 2023
Merged

An option to output SEQ field for secondary alignment #687

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f9e37e4
a new option --secondary-seq to output SEQ field for secondary alignm…
mikolmogorov Nov 25, 2020
395aea0
comments removed
mikolmogorov Nov 25, 2020
01cb5dd
merge 2.24
mikolmogorov Feb 17, 2023
3bda73b
Merge branch 'master' into master
lh3 Apr 21, 2023
55aa500
Fixed a conflict in #687
lh3 Apr 21, 2023
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10 changes: 6 additions & 4 deletions format.c
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Original file line number Diff line number Diff line change
Expand Up @@ -370,14 +370,16 @@ static void write_sam_cigar(kstring_t *s, int sam_flag, int in_tag, int qlen, co
clip_len[0] = r->rev? qlen - r->qe : r->qs;
clip_len[1] = r->rev? r->qs : qlen - r->qe;
if (in_tag) {
int clip_char = (sam_flag&0x800) && !(opt_flag&MM_F_SOFTCLIP)? 5 : 4;
int clip_char = ((sam_flag&0x800 || (sam_flag&0x100 && opt_flag&MM_F_SECONDARY_SEQ)) &&
!(opt_flag&MM_F_SOFTCLIP)) ? 5 : 4;
mm_sprintf_lite(s, "\tCG:B:I");
if (clip_len[0]) mm_sprintf_lite(s, ",%u", clip_len[0]<<4|clip_char);
for (k = 0; k < r->p->n_cigar; ++k)
mm_sprintf_lite(s, ",%u", r->p->cigar[k]);
if (clip_len[1]) mm_sprintf_lite(s, ",%u", clip_len[1]<<4|clip_char);
} else {
int clip_char = (sam_flag&0x800) && !(opt_flag&MM_F_SOFTCLIP)? 'H' : 'S';
int clip_char = ((sam_flag&0x800 || (sam_flag&0x100 && opt_flag&MM_F_SECONDARY_SEQ)) &&
!(opt_flag&MM_F_SOFTCLIP)) ? 'H' : 'S';
assert(clip_len[0] < qlen && clip_len[1] < qlen);
if (clip_len[0]) mm_sprintf_lite(s, "%d%c", clip_len[0], clip_char);
for (k = 0; k < r->p->n_cigar; ++k)
Expand Down Expand Up @@ -452,7 +454,7 @@ void mm_write_sam3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
if (cigar_in_tag) {
int slen;
if ((flag & 0x900) == 0 || (opt_flag & MM_F_SOFTCLIP)) slen = t->l_seq;
else if (flag & 0x100) slen = 0;
else if ((flag & 0x100) && !(opt_flag & MM_F_SECONDARY_SEQ)) slen = 0;
else slen = r->qe - r->qs;
mm_sprintf_lite(s, "%dS%dN", slen, r->re - r->rs);
} else write_sam_cigar(s, flag, 0, t->l_seq, r, opt_flag);
Expand Down Expand Up @@ -493,7 +495,7 @@ void mm_write_sam3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
mm_sprintf_lite(s, "\t");
if (t->qual) sam_write_sq(s, t->qual, t->l_seq, r->rev, 0);
else mm_sprintf_lite(s, "*");
} else if (flag & 0x100) {
} else if ((flag & 0x100) && !(opt_flag & MM_F_SECONDARY_SEQ)){
mm_sprintf_lite(s, "*\t*");
} else {
sam_write_sq(s, t->seq + r->qs, r->qe - r->qs, r->rev, r->rev);
Expand Down
2 changes: 2 additions & 0 deletions main.c
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Expand Up @@ -76,6 +76,7 @@ static ko_longopt_t long_options[] = {
{ "chain-skip-scale",ko_required_argument,351 },
{ "print-chains", ko_no_argument, 352 },
{ "no-hash-name", ko_no_argument, 353 },
{ "secondary-seq", ko_no_argument, 354 },
{ "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' },
{ "version", ko_no_argument, 'V' },
Expand Down Expand Up @@ -241,6 +242,7 @@ int main(int argc, char *argv[])
else if (c == 350) opt.q_occ_frac = atof(o.arg); // --q-occ-frac
else if (c == 352) mm_dbg_flag |= MM_DBG_PRINT_CHAIN; // --print-chains
else if (c == 353) opt.flag |= MM_F_NO_HASH_NAME; // --no-hash-name
else if (c == 354) opt.flag |= MM_F_SECONDARY_SEQ; // --secondary-seq
else if (c == 330) {
fprintf(stderr, "[WARNING] \033[1;31m --lj-min-ratio has been deprecated.\033[0m\n");
} else if (c == 314) { // --frag
Expand Down
1 change: 1 addition & 0 deletions minimap.h
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Expand Up @@ -43,6 +43,7 @@
#define MM_F_NO_INV (0x200000000LL)
#define MM_F_NO_HASH_NAME (0x400000000LL)
#define MM_F_SPLICE_OLD (0x800000000LL)
#define MM_F_SECONDARY_SEQ (0x1000000000LL) //output SEQ field for seqondary alignments using hard clipping

#define MM_I_HPC 0x1
#define MM_I_NO_SEQ 0x2
Expand Down