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Merge pull request #56 from mvdbeek/softclipping 

Implement -Y for soft clipping of supp. alignments
This commit is contained in:
Heng Li 2017-11-09 19:12:47 -05:00 committed by GitHub
parent 422b43374e 1cb0bf4bef
commit 032068a747
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GPG Key ID: 4AEE18F83AFDEB23
3 changed files with 13 additions and 5 deletions
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15
format.c
View File

@ -257,7 +257,7 @@ static inline const mm_reg1_t *get_sam_pri(int n_regs, const mm_reg1_t *regs)
return NULL;
}
static void write_sam_cigar(kstring_t *s, int sam_flag, int in_tag, int qlen, const mm_reg1_t *r)
static void write_sam_cigar(kstring_t *s, int sam_flag, int in_tag, int qlen, const mm_reg1_t *r, int opt_flag)
{
if (r->p == 0) {
mm_sprintf_lite(s, "*");
@ -266,14 +266,14 @@ 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)? 5 : 4;
int clip_char = (sam_flag&0x800 && !(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)? 'H' : 'S';
int clip_char = (sam_flag&0x800 && !(opt_flag&MM_F_SOFTCLIP))? 'H' : 'S';
if (clip_len[0]) mm_sprintf_lite(s, "%d%c", clip_len[0], clip_char);
for (k = 0; k < r->p->n_cigar; ++k)
mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MIDN"[r->p->cigar[k]&0xf]);
@ -348,7 +348,7 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
if (flag & 0x100) mm_sprintf_lite(s, "0S"); // secondary alignment
else if (flag & 0x800) mm_sprintf_lite(s, "%dS", r->re - r->rs); // supplementary alignment
else mm_sprintf_lite(s, "%dS", t->l_seq);
} else write_sam_cigar(s, flag, 0, t->l_seq, r);
} else write_sam_cigar(s, flag, 0, t->l_seq, r, opt_flag);
}
// write mate positions
@ -388,6 +388,11 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
else mm_sprintf_lite(s, "*");
} else if (flag & 0x100) {
mm_sprintf_lite(s, "*\t*");
} else if (opt_flag & MM_F_SOFTCLIP) {
sam_write_sq(s, t->seq, t->l_seq, r->rev, r->rev);
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 {
sam_write_sq(s, t->seq + r->qs, r->qe - r->qs, r->rev, r->rev);
mm_sprintf_lite(s, "\t");
@ -429,7 +434,7 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
if (r->p && (opt_flag & MM_F_OUT_CS))
write_cs(km, s, mi, t, r, !(opt_flag&MM_F_OUT_CS_LONG));
if (cigar_in_tag)
write_sam_cigar(s, flag, 1, t->l_seq, r);
write_sam_cigar(s, flag, 1, t->l_seq, r, opt_flag);
}
s->s[s->l] = 0; // we always have room for an extra byte (see str_enlarge)

2
main.c
View File

@ -109,6 +109,7 @@ int main(int argc, char *argv[])
else if (c == 'X') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
else if (c == 'a') opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
else if (c == 'Q') opt.flag |= MM_F_NO_QUAL;
else if (c == 'Y') opt.flag |= MM_F_SOFTCLIP;
else if (c == 'L') opt.flag |= MM_F_LONG_CIGAR;
else if (c == 'T') opt.sdust_thres = atoi(optarg);
else if (c == 'n') opt.min_cnt = atoi(optarg);
@ -232,6 +233,7 @@ int main(int argc, char *argv[])
fprintf(fp_help, " -R STR SAM read group line in a format like '@RG\\tID:foo\\tSM:bar' []\n");
fprintf(fp_help, " -c output CIGAR in PAF\n");
fprintf(fp_help, " --cs[=STR] output the cs tag; STR is 'short' (if absent) or 'long' [none]\n");
fprintf(fp_help, " -Y use soft clipping for supplementary alignments\n");
fprintf(fp_help, " -t INT number of threads [%d]\n", n_threads);
fprintf(fp_help, " -K NUM minibatch size for mapping [500M]\n");
// fprintf(fp_help, " -v INT verbose level [%d]\n", mm_verbose);

1
minimap.h
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@ -24,6 +24,7 @@
#define MM_F_LONG_CIGAR 0x10000
#define MM_F_INDEPEND_SEG 0x20000
#define MM_F_SPLICE_FLANK 0x40000
#define MM_F_SOFTCLIP 0x80000
#define MM_IDX_MAGIC "MMI\2"