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feat: add an option to output MD in the XA tag #439

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feat: add an option to output MD in the XA tag #439

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12 changes: 7 additions & 5 deletions bwape.c
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Original file line number Diff line number Diff line change
Expand Up @@ -621,7 +621,7 @@ ubyte_t *bwa_paired_sw(const bntseq_t *bns, const ubyte_t *_pacseq, int n_seqs,
return pacseq;
}

void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const fn_fa[2], pe_opt_t *popt, const char *rg_line)
void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const fn_fa[2], pe_opt_t *popt, const char *rg_line, int with_md)
{
extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
int i, j, n_seqs;
Expand Down Expand Up @@ -692,7 +692,7 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f

fprintf(stderr, "[bwa_sai2sam_pe_core] refine gapped alignments... ");
for (j = 0; j < 2; ++j)
bwa_refine_gapped(bns, n_seqs, seqs[j], pacseq);
bwa_refine_gapped(bns, n_seqs, seqs[j], pacseq, with_md);
fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
if (pac == 0) free(pacseq);

Expand Down Expand Up @@ -732,12 +732,12 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f

int bwa_sai2sam_pe(int argc, char *argv[])
{
int c;
int c, with_md = 0;
pe_opt_t *popt;
char *prefix, *rg_line = 0;

popt = bwa_init_pe_opt();
while ((c = getopt(argc, argv, "a:o:sPn:N:c:f:Ar:")) >= 0) {
while ((c = getopt(argc, argv, "a:o:sPn:N:c:f:Ar:d")) >= 0) {
switch (c) {
case 'r':
if ((rg_line = bwa_set_rg(optarg)) == 0) return 1;
Expand All @@ -751,6 +751,7 @@ int bwa_sai2sam_pe(int argc, char *argv[])
case 'c': popt->ap_prior = atof(optarg); break;
case 'f': xreopen(optarg, "w", stdout); break;
case 'A': popt->force_isize = 1; break;
case 'd': with_md = 1; break;
default: return 1;
}
}
Expand All @@ -768,6 +769,7 @@ int bwa_sai2sam_pe(int argc, char *argv[])
fprintf(stderr, " -P preload index into memory (for base-space reads only)\n");
fprintf(stderr, " -s disable Smith-Waterman for the unmapped mate\n");
fprintf(stderr, " -A disable insert size estimate (force -s)\n\n");
fprintf(stderr, " -d output the MD to each alignment in the XA tag, otherwise use \".\"\n\n");
fprintf(stderr, "Notes: 1. For SOLiD reads, <in1.fq> corresponds R3 reads and <in2.fq> to F3.\n");
fprintf(stderr, " 2. For reads shorter than 30bp, applying a smaller -o is recommended to\n");
fprintf(stderr, " to get a sensible speed at the cost of pairing accuracy.\n");
Expand All @@ -778,7 +780,7 @@ int bwa_sai2sam_pe(int argc, char *argv[])
fprintf(stderr, "[%s] fail to locate the index\n", __func__);
return 1;
}
bwa_sai2sam_pe_core(prefix, argv + optind + 1, argv + optind+3, popt, rg_line);
bwa_sai2sam_pe_core(prefix, argv + optind + 1, argv + optind+3, popt, rg_line, with_md);
free(prefix); free(popt);
return 0;
}
31 changes: 21 additions & 10 deletions bwase.c
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Expand Up @@ -284,11 +284,11 @@ void bwa_correct_trimmed(bwa_seq_t *s)
s->len = s->full_len;
}

void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq)
void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq, int with_md)
{
ubyte_t *pacseq;
int i, j, k;
kstring_t *str;
kstring_t *str = (kstring_t*)calloc(1, sizeof(kstring_t));

if (!_pacseq) {
pacseq = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
Expand All @@ -305,15 +305,25 @@ void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t
q->cigar = bwa_refine_gapped_core(bns->l_pac, pacseq, s->len, q->strand? s->rseq : s->seq, q->ref_shift, &q->pos, &n_cigar);
q->n_cigar = n_cigar;
if (q->cigar) s->multi[k++] = *q;
} else s->multi[k++] = *q;
} else {
s->multi[k++] = *q;
if (with_md) { // create the cigar, needed for bwa_cal_md1 below
q->n_cigar = 1;
q->cigar = calloc(q->n_cigar, sizeof(uint32_t));
q->cigar[0] = __cigar_create(FROM_M, s->len);
}
}
if (with_md) {
int nm;
q->md = bwa_cal_md1(q->n_cigar, q->cigar, s->len, q->pos, q->strand? s->rseq : s->seq, bns->l_pac, pacseq, str, &nm);
}
}
s->n_multi = k; // this squeezes out gapped alignments which failed the CIGAR generation
if (s->type == BWA_TYPE_NO_MATCH || s->type == BWA_TYPE_MATESW || s->n_gapo == 0) continue;
s->cigar = bwa_refine_gapped_core(bns->l_pac, pacseq, s->len, s->strand? s->rseq : s->seq, s->ref_shift, &s->pos, &s->n_cigar);
if (s->cigar == 0) s->type = BWA_TYPE_NO_MATCH;
}
// generate MD tag
str = (kstring_t*)calloc(1, sizeof(kstring_t));
for (i = 0; i != n_seqs; ++i) {
bwa_seq_t *s = seqs + i;
if (s->type != BWA_TYPE_NO_MATCH) {
Expand Down Expand Up @@ -504,7 +514,7 @@ void bwase_initialize()
for (i = 1; i != 256; ++i) g_log_n[i] = (int)(4.343 * log(i) + 0.5);
}

void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_fa, int n_occ, const char *rg_line)
void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_fa, int n_occ, const char *rg_line, int with_md)
{
extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
int i, n_seqs, m_aln;
Expand Down Expand Up @@ -557,7 +567,7 @@ void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_f
fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();

fprintf(stderr, "[bwa_aln_core] refine gapped alignments... ");
bwa_refine_gapped(bns, n_seqs, seqs, 0);
bwa_refine_gapped(bns, n_seqs, seqs, 0, with_md);
fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();

fprintf(stderr, "[bwa_aln_core] print alignments... ");
Expand All @@ -578,11 +588,12 @@ void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_f

int bwa_sai2sam_se(int argc, char *argv[])
{
int c, n_occ = 3;
int c, n_occ = 3, with_md = 0;
char *prefix, *rg_line = 0;
while ((c = getopt(argc, argv, "hn:f:r:")) >= 0) {
while ((c = getopt(argc, argv, "hdn:f:r:")) >= 0) {
switch (c) {
case 'h': break;
case 'd': with_md = 1; break;
case 'r':
if ((rg_line = bwa_set_rg(optarg)) == 0) return 1;
break;
Expand All @@ -593,14 +604,14 @@ int bwa_sai2sam_se(int argc, char *argv[])
}

if (optind + 3 > argc) {
fprintf(stderr, "Usage: bwa samse [-n max_occ] [-f out.sam] [-r RG_line] <prefix> <in.sai> <in.fq>\n");
fprintf(stderr, "Usage: bwa samse [-n max_occ] [-d] [-f out.sam] [-r RG_line] <prefix> <in.sai> <in.fq>\n");
return 1;
}
if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
fprintf(stderr, "[%s] fail to locate the index\n", __func__);
return 1;
}
bwa_sai2sam_se_core(prefix, argv[optind+1], argv[optind+2], n_occ, rg_line);
bwa_sai2sam_se_core(prefix, argv[optind+1], argv[optind+2], n_occ, rg_line, with_md);
free(prefix);
return 0;
}
2 changes: 1 addition & 1 deletion bwase.h
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Expand Up @@ -14,7 +14,7 @@ extern "C" {
// Calculate the approximate position of the sequence from the specified bwt with loaded suffix array.
void bwa_cal_pac_pos_core(const bntseq_t *bns, const bwt_t* bwt, bwa_seq_t* seq, const int max_mm, const float fnr);
// Refine the approximate position of the sequence to an actual placement for the sequence.
void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq);
void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq, int with_md);
// Backfill certain alignment properties mainly centering around number of matches.
void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s);
// Calculate the end position of a read given a certain sequence.
Expand Down
1 change: 1 addition & 0 deletions bwtaln.h
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Expand Up @@ -61,6 +61,7 @@ typedef struct {
int ref_shift;
bwtint_t pos;
bwa_cigar_t *cigar;
char *md;
} bwt_multi1_t;

typedef struct {
Expand Down
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