r751: optionally output MD (#118)
This commit is contained in:
Heng Li
parent
623b5d9d48
commit
8766d286df
88
format.c
88
format.c
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@ -133,31 +133,14 @@ void mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int
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free(str.s);
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}
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static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int no_iden)
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static void write_cs_core(kstring_t *s, const uint8_t *tseq, const uint8_t *qseq, const mm_reg1_t *r, char *tmp, int no_iden)
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{
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extern unsigned char seq_nt4_table[256];
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int i, q_off, t_off;
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uint8_t *qseq, *tseq;
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char *tmp;
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if (r->p == 0) return;
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mm_sprintf_lite(s, "\tcs:Z:");
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qseq = (uint8_t*)kmalloc(km, r->qe - r->qs);
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tseq = (uint8_t*)kmalloc(km, r->re - r->rs);
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tmp = (char*)kmalloc(km, r->re - r->rs > r->qe - r->qs? r->re - r->rs + 1 : r->qe - r->qs + 1);
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mm_idx_getseq(mi, r->rid, r->rs, r->re, tseq);
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if (!r->rev) {
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for (i = r->qs; i < r->qe; ++i)
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qseq[i - r->qs] = seq_nt4_table[(uint8_t)t->seq[i]];
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} else {
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for (i = r->qs; i < r->qe; ++i) {
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uint8_t c = seq_nt4_table[(uint8_t)t->seq[i]];
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qseq[r->qe - i - 1] = c >= 4? 4 : 3 - c;
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}
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}
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for (i = q_off = t_off = 0; i < r->p->n_cigar; ++i) {
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int j, op = r->p->cigar[i]&0xf, len = r->p->cigar[i]>>4;
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assert(op >= 0 && op <= 3);
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if (op == 0) {
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if (op == 0) { // match
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int l_tmp = 0;
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for (j = 0; j < len; ++j) {
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if (qseq[q_off + j] != tseq[t_off + j]) {
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@ -178,17 +161,17 @@ static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_
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} else mm_sprintf_lite(s, ":%d", l_tmp);
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}
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q_off += len, t_off += len;
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} else if (op == 1) {
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} else if (op == 1) { // insertion to ref
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for (j = 0, tmp[len] = 0; j < len; ++j)
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tmp[j] = "acgtn"[qseq[q_off + j]];
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mm_sprintf_lite(s, "+%s", tmp);
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q_off += len;
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} else if (op == 2) {
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} else if (op == 2) { // deletion from ref
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for (j = 0, tmp[len] = 0; j < len; ++j)
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tmp[j] = "acgtn"[tseq[t_off + j]];
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mm_sprintf_lite(s, "-%s", tmp);
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t_off += len;
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} else {
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} else { // intron
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assert(len >= 2);
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mm_sprintf_lite(s, "~%c%c%d%c%c", "acgtn"[tseq[t_off]], "acgtn"[tseq[t_off+1]],
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len, "acgtn"[tseq[t_off+len-2]], "acgtn"[tseq[t_off+len-1]]);
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@ -196,6 +179,59 @@ static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_
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}
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}
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assert(t_off == r->re - r->rs && q_off == r->qe - r->qs);
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}
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static void write_MD_core(kstring_t *s, const uint8_t *tseq, const uint8_t *qseq, const mm_reg1_t *r, char *tmp)
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{
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int i, q_off, t_off, l_MD = 0;
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mm_sprintf_lite(s, "\tMD:Z:");
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for (i = q_off = t_off = 0; i < r->p->n_cigar; ++i) {
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int j, op = r->p->cigar[i]&0xf, len = r->p->cigar[i]>>4;
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assert(op >= 0 && op <= 2); // introns (aka reference skips) are not supported
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if (op == 0) { // match
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for (j = 0; j < len; ++j) {
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if (qseq[q_off + j] != tseq[t_off + j]) {
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mm_sprintf_lite(s, "%d%c", l_MD, "ACGTN"[tseq[t_off + j]]);
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l_MD = 0;
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} else ++l_MD;
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}
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q_off += len, t_off += len;
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} else if (op == 1) { // insertion to ref
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q_off += len;
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} else if (op == 2) { // deletion from ref
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for (j = 0, tmp[len] = 0; j < len; ++j)
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tmp[j] = "ACGTN"[tseq[t_off + j]];
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mm_sprintf_lite(s, "%d^%s", l_MD, tmp);
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l_MD = 0;
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t_off += len;
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}
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}
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if (l_MD > 0) mm_sprintf_lite(s, "%d", l_MD);
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assert(t_off == r->re - r->rs && q_off == r->qe - r->qs);
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}
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static void write_cs_or_MD(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int no_iden, int is_MD)
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{
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extern unsigned char seq_nt4_table[256];
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int i;
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uint8_t *qseq, *tseq;
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char *tmp;
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if (r->p == 0) return;
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qseq = (uint8_t*)kmalloc(km, r->qe - r->qs);
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tseq = (uint8_t*)kmalloc(km, r->re - r->rs);
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tmp = (char*)kmalloc(km, r->re - r->rs > r->qe - r->qs? r->re - r->rs + 1 : r->qe - r->qs + 1);
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mm_idx_getseq(mi, r->rid, r->rs, r->re, tseq);
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if (!r->rev) {
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for (i = r->qs; i < r->qe; ++i)
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qseq[i - r->qs] = seq_nt4_table[(uint8_t)t->seq[i]];
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} else {
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for (i = r->qs; i < r->qe; ++i) {
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uint8_t c = seq_nt4_table[(uint8_t)t->seq[i]];
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qseq[r->qe - i - 1] = c >= 4? 4 : 3 - c;
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}
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}
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if (is_MD) write_MD_core(s, tseq, qseq, r, tmp);
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else write_cs_core(s, tseq, qseq, r, tmp, no_iden);
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kfree(km, qseq); kfree(km, tseq); kfree(km, tmp);
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}
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@ -236,8 +272,8 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
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for (k = 0; k < r->p->n_cigar; ++k)
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mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MIDN"[r->p->cigar[k]&0xf]);
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}
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if (r->p && (opt_flag & MM_F_OUT_CS))
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write_cs(km, s, mi, t, r, !(opt_flag&MM_F_OUT_CS_LONG));
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if (r->p && (opt_flag & (MM_F_OUT_CS|MM_F_OUT_MD)))
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write_cs_or_MD(km, s, mi, t, r, !(opt_flag&MM_F_OUT_CS_LONG), opt_flag&MM_F_OUT_MD);
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}
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static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp)
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@ -433,8 +469,8 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
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}
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}
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}
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if (r->p && (opt_flag & MM_F_OUT_CS))
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write_cs(km, s, mi, t, r, !(opt_flag&MM_F_OUT_CS_LONG));
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if (r->p && (opt_flag & (MM_F_OUT_CS|MM_F_OUT_MD)))
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write_cs_or_MD(km, s, mi, t, r, !(opt_flag&MM_F_OUT_CS_LONG), opt_flag&MM_F_OUT_MD);
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if (cigar_in_tag)
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write_sam_cigar(s, flag, 1, t->l_seq, r, opt_flag);
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}
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4
main.c
4
main.c
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@ -10,7 +10,7 @@
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#include "getopt.h"
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#endif
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#define MM_VERSION "2.9-r750-dirty"
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#define MM_VERSION "2.9-r751-dirty"
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#ifdef __linux__
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#include <sys/resource.h>
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@ -56,6 +56,7 @@ static struct option long_options[] = {
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{ "dual", required_argument, 0, 0 }, // 26
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{ "max-clip-ratio", required_argument, 0, 0 }, // 27
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{ "min-occ-floor", required_argument, 0, 0 }, // 28
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{ "MD", no_argument, 0, 0 }, // 29
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{ "help", no_argument, 0, 'h' },
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{ "max-intron-len", required_argument, 0, 'G' },
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{ "version", no_argument, 0, 'V' },
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@ -170,6 +171,7 @@ int main(int argc, char *argv[])
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else if (c == 0 && long_idx ==23) opt.flag |= MM_F_REV_ONLY; // --rev-only
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else if (c == 0 && long_idx ==27) opt.max_clip_ratio = atof(optarg); // --max-clip-ratio
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else if (c == 0 && long_idx ==28) opt.min_mid_occ = atoi(optarg); // --min-occ-floor
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else if (c == 0 && long_idx ==29) opt.flag |= MM_F_OUT_MD; // --MD
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else if (c == 0 && long_idx == 14) { // --frag
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yes_or_no(&opt, MM_F_FRAG_MODE, long_idx, optarg, 1);
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} else if (c == 0 && long_idx == 15) { // --secondary
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@ -29,6 +29,7 @@
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#define MM_F_REV_ONLY 0x200000
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#define MM_F_HEAP_SORT 0x400000
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#define MM_F_ALL_CHAINS 0x800000
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#define MM_F_OUT_MD 0x1000000
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#define MM_I_HPC 0x1
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#define MM_I_NO_SEQ 0x2
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@ -388,6 +388,9 @@ is given,
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.I short
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is assumed. [none]
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.TP
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.B --MD
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Output the MD tag (see the SAM spec).
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.TP
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.B -Y
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In SAM output, use soft clipping for supplementary alignments.
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.TP
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@ -559,6 +562,7 @@ cm i Number of minimizers on the chain
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s1 i Chaining score
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s2 i Chaining score of the best secondary chain
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NM i Total number of mismatches and gaps in the alignment
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MD Z To generate the ref sequence in the alignment
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AS i DP alignment score
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ms i DP score of the max scoring segment in the alignment
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nn i Number of ambiguous bases in the alignment
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