150 lines
4.9 KiB
C
150 lines
4.9 KiB
C
#include <stdarg.h>
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#include <stdlib.h>
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#include <string.h>
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#include <stdio.h>
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#include "mmpriv.h"
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static inline void str_enlarge(kstring_t *s, int l)
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{
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if (s->l + l + 1 > s->m) {
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s->m = s->l + l + 1;
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kroundup32(s->m);
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s->s = (char*)realloc(s->s, s->m);
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}
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}
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static inline void str_copy(kstring_t *s, const char *st, const char *en)
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{
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str_enlarge(s, en - st);
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memcpy(&s->s[s->l], st, en - st);
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s->l += en - st;
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}
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static void mm_sprintf_lite(kstring_t *s, const char *fmt, ...)
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{
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char buf[16]; // for integer to string conversion
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const char *p, *q;
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va_list ap;
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va_start(ap, fmt);
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for (q = p = fmt; *p; ++p) {
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if (*p == '%') {
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if (p > q) str_copy(s, q, p);
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++p;
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if (*p == 'd') {
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int c, i, l = 0;
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unsigned int x;
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c = va_arg(ap, int);
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x = c >= 0? c : -c;
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do { buf[l++] = x%10 + '0'; x /= 10; } while (x > 0);
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if (c < 0) buf[l++] = '-';
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str_enlarge(s, l);
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for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];
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} else if (*p == 's') {
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char *r = va_arg(ap, char*);
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str_copy(s, r, r + strlen(r));
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} else if (*p == 'c') {
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str_enlarge(s, 1);
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s->s[s->l++] = va_arg(ap, int);
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} else abort();
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q = p + 1;
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}
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}
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if (p > q) str_copy(s, q, p);
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va_end(ap);
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s->s[s->l] = 0;
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}
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static inline void write_tags(kstring_t *s, const mm_reg1_t *r)
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{
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mm_sprintf_lite(s, "\tcm:i:%d", r->cnt);
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if (r->p) mm_sprintf_lite(s, "\ts1:i:%d", r->score);
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if (r->parent == r->id) mm_sprintf_lite(s, "\ts2:i:%d", r->subsc);
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if (r->split) mm_sprintf_lite(s, "\tzd:i:%d", r->split);
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if (r->p) mm_sprintf_lite(s, "\tNM:i:%d\tms:i:%d\tAS:i:%d\tnn:i:%d", r->p->n_diff, r->p->dp_max, r->p->dp_score, r->p->n_ambi);
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}
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void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_reg1_t *r)
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{
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s->l = 0;
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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]);
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if (mi->seq[r->rid].name) mm_sprintf_lite(s, "%s", mi->seq[r->rid].name);
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else mm_sprintf_lite(s, "%d", r->rid);
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mm_sprintf_lite(s, "\t%d\t%d\t%d", mi->seq[r->rid].len, r->rs, r->re);
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if (r->p) mm_sprintf_lite(s, "\t%d\t%d", r->p->blen - r->p->n_ambi - r->p->n_diff, r->p->blen);
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else mm_sprintf_lite(s, "\t%d\t%d", r->score, r->re - r->rs > r->qe - r->qs? r->re - r->rs : r->qe - r->qs);
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mm_sprintf_lite(s, "\t%d", r->mapq);
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write_tags(s, r);
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if (r->p) {
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uint32_t k;
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mm_sprintf_lite(s, "\tcg:Z:");
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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, "MID"[r->p->cigar[k]&0xf]);
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}
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}
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static char comp_tab[] = {
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0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
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16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
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32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
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48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63,
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64, 'T', 'V', 'G', 'H', 'E', 'F', 'C', 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O',
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'P', 'Q', 'Y', 'S', 'A', 'A', 'B', 'W', 'X', 'R', 'Z', 91, 92, 93, 94, 95,
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64, 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o',
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'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', 123, 124, 125, 126, 127
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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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{
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if (rev) {
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int i;
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str_enlarge(s, l);
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for (i = 0; i < l; ++i) {
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int c = seq[l - 1 - i];
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s->s[s->l + i] = c < 128 && comp? comp_tab[c] : c;
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}
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s->l += l;
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} else str_copy(s, seq, seq + l);
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}
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void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_reg1_t *r)
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{
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int flag = 0;
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s->l = 0;
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if (r == 0) {
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mm_sprintf_lite(s, "%s\t0\t*\t0\t0\t*\t*\t0\t0\t", t->name);
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sam_write_sq(s, t->seq, t->l_seq, 0, 0);
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mm_sprintf_lite(s, "\t");
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if (t->qual) sam_write_sq(s, t->qual, t->l_seq, 0, 0);
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else mm_sprintf_lite(s, "*");
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} else {
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if (r->rev) flag |= 0x10;
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if (r->parent != r->id) flag |= 0x100;
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else if (!r->sam_pri) flag |= 0x800;
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mm_sprintf_lite(s, "%s\t%d\t%s\t%d\t%d\t", t->name, flag, mi->seq[r->rid].name, r->rs+1, r->mapq);
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if (r->p) { // TODO: using hard clippings
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uint32_t k, clip_len = r->rev? t->l_seq - r->qe : r->qs;
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int clip_char = (flag&0x800)? 'H' : 'S';
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if (clip_len) mm_sprintf_lite(s, "%d%c", clip_len, clip_char);
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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, "MID"[r->p->cigar[k]&0xf]);
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clip_len = r->rev? r->qs : t->l_seq - r->qe;
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if (clip_len) mm_sprintf_lite(s, "%d%c", clip_len, clip_char);
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} else mm_sprintf_lite(s, "*");
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mm_sprintf_lite(s, "\t*\t0\t0\t");
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if ((flag & 0x900) == 0) {
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sam_write_sq(s, t->seq, t->l_seq, r->rev, r->rev);
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mm_sprintf_lite(s, "\t");
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if (t->qual) sam_write_sq(s, t->qual, t->l_seq, r->rev, 0);
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else mm_sprintf_lite(s, "*");
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} else if (flag & 0x100) {
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mm_sprintf_lite(s, "*\t*");
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} else {
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sam_write_sq(s, t->seq + r->qs, r->qe - r->qs, r->rev, r->rev);
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mm_sprintf_lite(s, "\t");
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if (t->qual) sam_write_sq(s, t->qual + r->qs, r->qe - r->qs, r->rev, 0);
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else mm_sprintf_lite(s, "*");
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}
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write_tags(s, r);
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}
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}
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