| c1100b9b |
#include <string.h>
#include <ctype.h>
#include <stdio.h>
#include "kstring.h"
#include "bcf.h"
bcf_t *bcf_open(const char *fn, const char *mode)
{
bcf_t *b;
b = calloc(1, sizeof(bcf_t));
if (strchr(mode, 'w')) {
b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdout), mode);
} else {
b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdout), mode);
}
return b;
}
int bcf_close(bcf_t *b)
{
int ret;
if (b == 0) return 0;
ret = bgzf_close(b->fp);
free(b);
return ret;
}
int bcf_hdr_write(bcf_t *b, const bcf_hdr_t *h)
{
if (b == 0 || h == 0) return -1;
bgzf_write(b->fp, "BCF\4", 4);
bgzf_write(b->fp, &h->l_nm, 4);
bgzf_write(b->fp, h->name, h->l_nm);
bgzf_write(b->fp, &h->l_smpl, 4);
bgzf_write(b->fp, h->sname, h->l_smpl);
bgzf_write(b->fp, &h->l_txt, 4);
bgzf_write(b->fp, h->txt, h->l_txt);
bgzf_flush(b->fp);
return 16 + h->l_nm + h->l_smpl + h->l_txt;
}
bcf_hdr_t *bcf_hdr_read(bcf_t *b)
{
uint8_t magic[4];
bcf_hdr_t *h;
if (b == 0) return 0;
h = calloc(1, sizeof(bcf_hdr_t));
bgzf_read(b->fp, magic, 4);
bgzf_read(b->fp, &h->l_nm, 4);
h->name = malloc(h->l_nm);
bgzf_read(b->fp, h->name, h->l_nm);
bgzf_read(b->fp, &h->l_smpl, 4);
h->sname = malloc(h->l_smpl);
bgzf_read(b->fp, h->sname, h->l_smpl);
bgzf_read(b->fp, &h->l_txt, 4);
h->txt = malloc(h->l_txt);
bgzf_read(b->fp, h->txt, h->l_txt);
bcf_hdr_sync(h);
return h;
}
void bcf_hdr_destroy(bcf_hdr_t *h)
{
if (h == 0) return;
free(h->name); free(h->sname); free(h->txt); free(h->ns); free(h->sns);
free(h);
}
static inline char **cnt_null(int l, char *str, int *_n)
{
int n = 0;
char *p, **list;
*_n = 0;
if (l == 0 || str == 0) return 0;
for (p = str; p != str + l; ++p)
if (*p == 0) ++n;
*_n = n;
list = calloc(n, sizeof(void*));
list[0] = str;
for (p = str, n = 1; p < str + l - 1; ++p)
if (*p == 0) list[n++] = p + 1;
return list;
}
int bcf_hdr_sync(bcf_hdr_t *b)
{
if (b == 0) return -1;
if (b->ns) free(b->ns);
if (b->sns) free(b->sns);
if (b->l_nm) b->ns = cnt_null(b->l_nm, b->name, &b->n_ref);
else b->ns = 0, b->n_ref = 0;
b->sns = cnt_null(b->l_smpl, b->sname, &b->n_smpl);
return 0;
}
int bcf_sync(bcf1_t *b)
{
char *p, *tmp[5];
int i, n, n_smpl = b->n_smpl;
ks_tokaux_t aux;
// set ref, alt, flt, info, fmt
b->ref = b->alt = b->flt = b->info = b->fmt = 0;
for (p = b->str, n = 0; p < b->str + b->l_str; ++p) {
if (*p == 0 && p+1 != b->str + b->l_str) {
if (n == 5) {
++n;
break;
} else tmp[n++] = p + 1;
}
}
if (n != 5) {
fprintf(stderr, "[%s] incorrect number of fields (%d != 5) at %d:%d\n", __func__, n, b->tid, b->pos);
return -1;
}
b->ref = tmp[0]; b->alt = tmp[1]; b->flt = tmp[2]; b->info = tmp[3]; b->fmt = tmp[4];
// set n_alleles
if (*b->alt == 0) b->n_alleles = 1;
else {
for (p = b->alt, n = 1; *p; ++p)
if (*p == ',') ++n;
b->n_alleles = n + 1;
}
// set n_gi and gi[i].fmt
for (p = b->fmt, n = 1; *p; ++p)
if (*p == ':') ++n;
if (n > b->m_gi) {
int old_m = b->m_gi;
b->m_gi = n;
kroundup32(b->m_gi);
b->gi = realloc(b->gi, b->m_gi * sizeof(bcf_ginfo_t));
memset(b->gi + old_m, 0, (b->m_gi - old_m) * sizeof(bcf_ginfo_t));
}
b->n_gi = n;
for (p = kstrtok(b->fmt, ":", &aux), n = 0; p; p = kstrtok(0, 0, &aux))
b->gi[n++].fmt = bcf_str2int(p, aux.p - p);
// set gi[i].len
for (i = 0; i < b->n_gi; ++i) {
if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2;
} else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
b->gi[i].len = 2;
} else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)) {
b->gi[i].len = 1;
} else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
b->gi[i].len = 4;
} else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2 * 4;
}
b->gi[i].data = realloc(b->gi[i].data, n_smpl * b->gi[i].len);
}
return 0;
}
int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b)
{
int i, l = 0;
if (b == 0) return -1;
bgzf_write(bp->fp, &b->tid, 4);
bgzf_write(bp->fp, &b->pos, 4);
bgzf_write(bp->fp, &b->qual, 4);
bgzf_write(bp->fp, &b->l_str, 4);
bgzf_write(bp->fp, b->str, b->l_str);
l = 12 + b->l_str;
for (i = 0; i < b->n_gi; ++i) {
bgzf_write(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
l += b->gi[i].len * h->n_smpl;
}
return l;
}
int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b)
{
int i, l = 0;
if (b == 0) return -1;
if (bgzf_read(bp->fp, &b->tid, 4) == 0) return -1;
b->n_smpl = h->n_smpl;
bgzf_read(bp->fp, &b->pos, 4);
bgzf_read(bp->fp, &b->qual, 4);
bgzf_read(bp->fp, &b->l_str, 4);
if (b->l_str > b->m_str) {
b->m_str = b->l_str;
kroundup32(b->m_str);
b->str = realloc(b->str, b->m_str);
}
bgzf_read(bp->fp, b->str, b->l_str);
l = 12 + b->l_str;
if (bcf_sync(b) < 0) return -2;
for (i = 0; i < b->n_gi; ++i) {
bgzf_read(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
l += b->gi[i].len * h->n_smpl;
}
return l;
}
int bcf_destroy(bcf1_t *b)
{
int i;
if (b == 0) return -1;
free(b->str);
for (i = 0; i < b->m_gi; ++i)
free(b->gi[i].data);
free(b->gi);
free(b);
return 0;
}
static inline void fmt_str(const char *p, kstring_t *s)
{
if (*p == 0) kputc('.', s);
else kputs(p, s);
}
void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
{
int i, j, x;
s->l = 0;
if (h->n_ref) kputs(h->ns[b->tid], s);
else kputw(b->tid, s);
kputc('\t', s);
kputw(b->pos + 1, s); kputc('\t', s);
fmt_str(b->str, s); kputc('\t', s);
fmt_str(b->ref, s); kputc('\t', s);
fmt_str(b->alt, s); kputc('\t', s);
ksprintf(s, "%.3g", b->qual); kputc('\t', s);
fmt_str(b->flt, s); kputc('\t', s);
fmt_str(b->info, s);
if (b->fmt[0]) {
kputc('\t', s);
fmt_str(b->fmt, s);
}
x = b->n_alleles * (b->n_alleles + 1) / 2;
if (b->n_gi == 0) return;
int iPL = -1;
if ( b->n_alleles > 2 ) {
for (i=0; i<b->n_gi; i++) {
if ( b->gi[i].fmt == bcf_str2int("PL", 2) ) {
iPL = i;
break;
}
}
}
for (j = 0; j < h->n_smpl; ++j) {
int ploidy = b->ploidy ? b->ploidy[j] : 2;
kputc('\t', s);
for (i = 0; i < b->n_gi; ++i) {
if (i) kputc(':', s);
if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
uint8_t *d = (uint8_t*)b->gi[i].data + j * x;
int k;
if ( ploidy==1 )
for (k=0; k<b->n_alleles; k++)
{
if (k>0) kputc(',', s);
kputw(d[(k+1)*(k+2)/2-1], s);
}
else
for (k = 0; k < x; ++k) {
if (k > 0) kputc(',', s);
kputw(d[k], s);
}
} else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
kputw(((uint16_t*)b->gi[i].data)[j], s);
} else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
kputw(((uint8_t*)b->gi[i].data)[j], s);
} else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
kputw(((int32_t*)b->gi[i].data)[j], s);
} else if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
int y = ((uint8_t*)b->gi[i].data)[j];
if ( ploidy==1 )
{
if ( y>>7&1 )
kputc('.', s);
else
kputc('0' + (y>>3&7), s);
}
else
{
if ( y>>7&1 )
kputsn("./.", 3, s);
else {
kputc('0' + (y>>3&7), s);
kputc("/|"[y>>6&1], s);
kputc('0' + (y&7), s);
}
}
} else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
float *d = (float*)b->gi[i].data + j * x;
int k;
//printf("- %lx\n", d);
for (k = 0; k < x; ++k) {
if (k > 0) kputc(',', s);
ksprintf(s, "%.2f", d[k]);
}
} else kputc('.', s); // custom fields
}
}
}
char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b)
{
kstring_t s;
s.l = s.m = 0; s.s = 0;
bcf_fmt_core(h, b, &s);
return s.s;
}
int bcf_append_info(bcf1_t *b, const char *info, int l)
{
int shift = b->fmt - b->str;
int l_fmt = b->l_str - shift;
char *ori = b->str;
if (b->l_str + l > b->m_str) { // enlarge if necessary
b->m_str = b->l_str + l;
kroundup32(b->m_str);
b->str = realloc(b->str, b->m_str);
}
memmove(b->str + shift + l, b->str + shift, l_fmt); // move the FORMAT field
memcpy(b->str + shift - 1, info, l); // append to the INFO field
b->str[shift + l - 1] = '\0';
b->fmt = b->str + shift + l;
b->l_str += l;
if (ori != b->str) bcf_sync(b); // synchronize when realloc changes the pointer
return 0;
}
int remove_tag(char *str, const char *tag, char delim)
{
char *tmp = str, *p;
int len_diff = 0, ori_len = strlen(str);
while ( *tmp && (p = strstr(tmp,tag)) )
{
if ( p>str )
{
if ( *(p-1)!=delim ) { tmp=p+1; continue; } // shared substring
p--;
}
char *q=p+1;
while ( *q && *q!=delim ) q++;
if ( p==str && *q ) q++; // the tag is first, don't move the delim char
len_diff += q-p;
if ( ! *q ) { *p = 0; break; } // the tag was last, no delim follows
else
memmove(p,q,ori_len-(int)(p-str)-(int)(q-p)); // *q==delim
}
if ( len_diff==ori_len )
str[0]='.', str[1]=0, len_diff--;
return len_diff;
}
void rm_info(kstring_t *s, const char *key)
{
char *p = s->s;
int n = 0;
while ( n<4 )
{
if ( !*p ) n++;
p++;
}
char *q = p+1;
while ( *q && q-s->s<s->l ) q++;
int nrm = remove_tag(p, key, ';');
if ( nrm )
memmove(q-nrm, q, s->s+s->l-q+1);
s->l -= nrm;
}
int bcf_cpy(bcf1_t *r, const bcf1_t *b)
{
char *t1 = r->str;
bcf_ginfo_t *t2 = r->gi;
int i, t3 = r->m_str, t4 = r->m_gi;
*r = *b;
r->str = t1; r->gi = t2; r->m_str = t3; r->m_gi = t4;
if (r->m_str < b->m_str) {
r->m_str = b->m_str;
r->str = realloc(r->str, r->m_str);
}
memcpy(r->str, b->str, r->m_str);
bcf_sync(r); // calling bcf_sync() is simple but inefficient
for (i = 0; i < r->n_gi; ++i)
memcpy(r->gi[i].data, b->gi[i].data, r->n_smpl * r->gi[i].len);
return 0;
}
int bcf_is_indel(const bcf1_t *b)
{
char *p;
if (strlen(b->ref) > 1) return 1;
for (p = b->alt; *p; ++p)
if (*p != ',' && p[1] != ',' && p[1] != '\0')
return 1;
return 0;
}
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