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format.c
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format.c
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#include <stdarg.h>
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <stdio.h>
#include <math.h>
#include "kalloc.h"
#include "mgpriv.h"
static inline void str_enlarge(kstring_t *s, int l)
{
if (s->l + l + 1 > s->m) {
s->m = s->l + l + 1;
kroundup32(s->m);
s->s = (char*)realloc(s->s, s->m);
}
}
static inline void str_copy(kstring_t *s, const char *st, const char *en)
{
str_enlarge(s, en - st);
memcpy(&s->s[s->l], st, en - st);
s->l += en - st;
}
void mg_sprintf_lite(kstring_t *s, const char *fmt, ...)
{
char buf[16]; // for integer to string conversion
const char *p, *q;
va_list ap;
va_start(ap, fmt);
for (q = p = fmt; *p; ++p) {
if (*p == '%') {
if (p > q) str_copy(s, q, p);
++p;
if (*p == 'd') {
int c, i, l = 0;
unsigned int x;
c = va_arg(ap, int);
x = c >= 0? c : -c;
do { buf[l++] = x%10 + '0'; x /= 10; } while (x > 0);
if (c < 0) buf[l++] = '-';
str_enlarge(s, l);
for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];
} else if (*p == 'u') {
int i, l = 0;
uint32_t x;
x = va_arg(ap, uint32_t);
do { buf[l++] = x%10 + '0'; x /= 10; } while (x > 0);
str_enlarge(s, l);
for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];
} else if (*p == 's') {
char *r = va_arg(ap, char*);
str_copy(s, r, r + strlen(r));
} else if (*p == 'c') {
str_enlarge(s, 1);
s->s[s->l++] = va_arg(ap, int);
} else abort();
q = p + 1;
}
}
if (p > q) str_copy(s, q, p);
va_end(ap);
s->s[s->l] = 0;
}
void mg_print_lchain(FILE *fp, const mg_idx_t *gi, int n_lc, const mg_lchain_t *lc, const mg128_t *a, const char *qname)
{
kstring_t str = {0,0,0};
int i, j;
for (i = 0; i < n_lc; ++i) {
const mg_lchain_t *p = &lc[i];
int mlen, blen, span = a[p->off].y>>32&0xff;
mlen = blen = span;
for (j = 1; j < p->cnt; ++j) {
int ql = (int32_t)a[p->off + j].y - (int32_t)a[p->off + j - 1].y;
int pl = (int32_t)a[p->off + j].x - (int32_t)a[p->off + j - 1].x;
blen += pl > ql? pl : ql;
mlen += pl > span && ql > span? span : pl < ql? pl : ql;
}
str.l = 0;
mg_sprintf_lite(&str, "LC\t%s\t%d\t%d\t%c\t%s\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t", qname, p->qs, p->qe, "+-"[p->v&1], gi->g->seg[p->v>>1].name, gi->g->seg[p->v>>1].len,
p->rs, p->re, p->score, mlen, blen, p->cnt);
for (j = 0; j < p->cnt; ++j)
mg_sprintf_lite(&str, "%d,", (int32_t)a[p->off + j].y);
mg_sprintf_lite(&str, "\t");
for (j = 0; j < p->cnt; ++j)
mg_sprintf_lite(&str, "%d,", (int32_t)a[p->off + j].x);
mg_sprintf_lite(&str, "\t");
for (j = 0; j < p->cnt; ++j)
mg_sprintf_lite(&str, "%d,", (int32_t)(a[p->off + j].y>>MG_SEED_OCC_SHIFT));
mg_sprintf_lite(&str, "\n");
fwrite(str.s, 1, str.l, fp);
}
free(str.s);
}
void mg_write_gaf(kstring_t *s, const gfa_t *g, const mg_gchains_t *gs, int32_t n_seg, const int32_t *qlens, const char *qname, uint64_t flag, void *km)
{
int32_t i, j, qlen, rev_sign = 0;
s->l = 0;
for (i = 0, qlen = 0; i < n_seg; ++i) qlen += qlens[i];
if ((gs == 0 || gs->n_gc == 0) && (flag&MG_M_SHOW_UNMAP)) {
mg_sprintf_lite(s, "%s", qname);
if ((flag&MG_M_FRAG_MERGE) && n_seg == 2 && s->l > 2 && s->s[s->l-1] == '1' && s->s[s->l-2] == '/') s->l -= 2;
mg_sprintf_lite(s, "\t%d\t0\t0\t*\t*\t0\t0\t0\t0\t0\t0\n", qlen);
return;
}
if (gs == 0) return;
for (i = 0; i < gs->n_gc; ++i) {
const mg_gchain_t *p = &gs->gc[i];
int32_t sign_pos, compact;
if (p->id != p->parent && !(flag&MG_M_PRINT_2ND)) continue;
if (p->cnt == 0) continue;
mg_sprintf_lite(s, "%s", qname);
if ((flag&MG_M_FRAG_MERGE) && n_seg == 2 && s->l > 2 && s->s[s->l-1] == '1' && s->s[s->l-2] == '/') s->l -= 2;
mg_sprintf_lite(s, "\t%d\t%d\t%d\t+\t", qlen, p->qs, p->qe);
assert(p->cnt > 0);
sign_pos = s->l - 2;
if (flag & MG_M_VERTEX_COOR) {
compact = 0;
for (j = 0; j < p->cnt; ++j) {
const mg_llchain_t *q = &gs->lc[p->off + j];
mg_sprintf_lite(s, "%c%s", "><"[q->v&1], g->seg[q->v>>1].name);
}
} else {
int32_t last_pnid = -1, st = -1, en = -1, rev = -1;
compact = flag&MG_M_NO_COMP_PATH? 0 : 1;
for (j = 0; j < p->cnt; ++j) {
const mg_llchain_t *q;
const gfa_seg_t *t;
assert(p->off + j < gs->n_lc);
q = &gs->lc[p->off + j];
t = &g->seg[q->v>>1];
if (t->snid < 0) { // no stable ID; write the vertex coordinate
compact = 0;
if (last_pnid >= 0) mg_sprintf_lite(s, "%c%s:%d-%d", "><"[rev], g->sseq[last_pnid].name, st, en);
last_pnid = -1, st = -1, en = -1, rev = -1;
mg_sprintf_lite(s, "%c%s", "><"[q->v&1], g->seg[q->v>>1].name);
} else {
int cont = 0;
if (last_pnid >= 0 && t->snid == last_pnid && (q->v&1) == rev) { // same stable sequence and same strand
if (!(q->v&1)) { // forward strand
if (t->soff == en)
en = t->soff + t->len, cont = 1;
} else { // reverse strand
if (t->soff + t->len == st)
st = t->soff, cont = 1;
}
}
if (cont == 0) {
if (last_pnid >= 0) compact = 0;
if (last_pnid >= 0) mg_sprintf_lite(s, "%c%s:%d-%d", "><"[rev], g->sseq[last_pnid].name, st, en);
last_pnid = t->snid, rev = q->v&1, st = t->soff, en = st + t->len;
}
}
}
if (last_pnid >= 0) {
if (g->sseq[last_pnid].rank != 0 || g->sseq[last_pnid].min != 0)
compact = 0;
if (!compact) mg_sprintf_lite(s, "%c%s:%d-%d", "><"[rev], g->sseq[last_pnid].name, st, en);
} else compact = 0;
}
if (compact) {
int32_t rev = gs->lc[p->off].v&1;
const gfa_seg_t *t = &g->seg[gs->lc[rev? p->off + p->cnt - 1 : p->off].v>>1];
const gfa_sseq_t *ps = &g->sseq[t->snid];
mg_sprintf_lite(s, "%s\t%d\t", ps->name, ps->max);
if (rev) {
rev_sign = 1;
s->s[sign_pos] = '-';
mg_sprintf_lite(s, "%d\t%d", t->soff + (p->plen - p->pe), t->soff + (p->plen - p->ps));
} else {
mg_sprintf_lite(s, "%d\t%d", t->soff + p->ps, t->soff + p->pe);
}
} else mg_sprintf_lite(s, "\t%d\t%d\t%d", p->plen, p->ps, p->pe);
if (p->p) mg_sprintf_lite(s, "\t%d\t%d\t%d", p->p->mlen, p->p->blen, p->mapq);
else mg_sprintf_lite(s, "\t%d\t%d\t%d", p->mlen, p->blen, p->mapq);
mg_sprintf_lite(s, "\ttp:A:%c", p->id == p->parent? 'P' : 'S');
if (p->p) mg_sprintf_lite(s, "\tNM:i:%d", p->p->blen - p->p->mlen);
mg_sprintf_lite(s, "\tcm:i:%d\ts1:i:%d\ts2:i:%d", p->n_anchor, p->score, p->subsc);
if (p->div >= 0.0f && p->div <= 1.0f) {
char buf[16];
if (p->div == 0.0f) buf[0] = '0', buf[1] = 0;
else snprintf(buf, 16, "%.4f", p->div);
mg_sprintf_lite(s, "\tdv:f:%s", buf);
}
if (n_seg > 1) {
mg_sprintf_lite(s, "\tql:B:i");
for (j = 0; j < n_seg; ++j) mg_sprintf_lite(s, ",%d", qlens[j]);
}
if (p->p) {
mg_sprintf_lite(s, "\tcg:Z:");
if (rev_sign)
for (j = p->p->n_cigar - 1; j >= 0; --j)
mg_sprintf_lite(s, "%d%c", (int32_t)(p->p->cigar[j]>>4), "MIDNSHP=XB"[p->p->cigar[j]&0xf]);
else
for (j = 0; j < p->p->n_cigar; ++j)
mg_sprintf_lite(s, "%d%c", (int32_t)(p->p->cigar[j]>>4), "MIDNSHP=XB"[p->p->cigar[j]&0xf]);
}
mg_sprintf_lite(s, "\n");
if ((mg_dbg_flag & MG_DBG_LCHAIN) || (flag & MG_M_WRITE_LCHAIN)) {
char buf[16];
for (j = 0; j < p->cnt; ++j) {
const mg_llchain_t *lc = &gs->lc[p->off + j];
mg_sprintf_lite(s, "*\t%c%s\t%d\t%d", "><"[lc->v&1], g->seg[lc->v>>1].name, g->seg[lc->v>>1].len, lc->cnt);
if (lc->cnt > 0) {
double div;
int32_t q_span = (int32_t)(gs->a[lc->off].y>>32&0xff);
int32_t n = (int32_t)(gs->a[lc->off + lc->cnt - 1].x>>32) - (int32_t)(gs->a[lc->off].x>>32) + 1;
div = n == lc->cnt? 0.0 : (n > lc->cnt? log((double)n / lc->cnt) : log((double)lc->cnt / n)) / q_span;
if (div == 0.0) buf[0] = '0', buf[1] = 0;
else snprintf(buf, 16, "%.4f", div);
mg_sprintf_lite(s, "\t%s", buf);
mg_sprintf_lite(s, "\t%d\t%d", (int32_t)gs->a[lc->off].x + 1 - q_span, (int32_t)gs->a[lc->off + lc->cnt - 1].x + 1);
mg_sprintf_lite(s, "\t%d\t%d", (int32_t)gs->a[lc->off].y + 1 - q_span, (int32_t)gs->a[lc->off + lc->cnt - 1].y + 1);
if (flag & MG_M_WRITE_MZ) {
int32_t i, last;
last = (int32_t)gs->a[lc->off].x + 1 - q_span;
mg_sprintf_lite(s, "\t%d\t", q_span);
for (i = 1; i < lc->cnt; ++i) {
int32_t x = (int32_t)gs->a[lc->off + i].x + 1 - q_span;
if (i > 1) mg_sprintf_lite(s, ",");
mg_sprintf_lite(s, "%d", x - last);
last = x;
}
last = (int32_t)gs->a[lc->off].y + 1 - q_span;
mg_sprintf_lite(s, "\t");
for (i = 1; i < lc->cnt; ++i) {
int32_t x = (int32_t)gs->a[lc->off + i].y + 1 - q_span;
if (i > 1) mg_sprintf_lite(s, ",");
mg_sprintf_lite(s, "%d", x - last);
last = x;
}
}
}
mg_sprintf_lite(s, "\n");
}
}
}
}