| c1100b9b |
#include <zlib.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "bcf.h"
#include "kstring.h"
#include "kseq.h"
KSTREAM_INIT(gzFile, gzread, 4096)
typedef struct {
gzFile fp;
FILE *fpout;
kstream_t *ks;
void *refhash;
kstring_t line;
int max_ref;
} vcf_t;
bcf_hdr_t *vcf_hdr_read(bcf_t *bp)
{
kstring_t meta, smpl;
int dret;
vcf_t *v;
bcf_hdr_t *h;
if (!bp->is_vcf) return bcf_hdr_read(bp);
h = calloc(1, sizeof(bcf_hdr_t));
v = (vcf_t*)bp->v;
v->line.l = 0;
memset(&meta, 0, sizeof(kstring_t));
memset(&smpl, 0, sizeof(kstring_t));
while (ks_getuntil(v->ks, '\n', &v->line, &dret) >= 0) {
if (v->line.l < 2) continue;
if (v->line.s[0] != '#') {
free(meta.s);
free(smpl.s);
free(h);
return 0; // no sample line
}
if (v->line.s[0] == '#' && v->line.s[1] == '#') {
kputsn(v->line.s, v->line.l, &meta); kputc('\n', &meta);
} else if (v->line.s[0] == '#') {
int k;
ks_tokaux_t aux;
char *p;
for (p = kstrtok(v->line.s, "\t\n", &aux), k = 0; p; p = kstrtok(0, 0, &aux), ++k) {
if (k >= 9) {
kputsn(p, aux.p - p, &smpl);
kputc('\0', &smpl);
}
}
break;
}
}
kputc('\0', &meta);
h->name = 0;
h->sname = smpl.s; h->l_smpl = smpl.l;
h->txt = meta.s; h->l_txt = meta.l;
bcf_hdr_sync(h);
return h;
}
bcf_t *vcf_open(const char *fn, const char *mode)
{
bcf_t *bp;
vcf_t *v;
if (strchr(mode, 'b')) return bcf_open(fn, mode);
bp = calloc(1, sizeof(bcf_t));
v = calloc(1, sizeof(vcf_t));
bp->is_vcf = 1;
bp->v = v;
v->refhash = bcf_str2id_init();
if (strchr(mode, 'r')) {
v->fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
v->ks = ks_init(v->fp);
} else if (strchr(mode, 'w'))
v->fpout = strcmp(fn, "-")? fopen(fn, "w") : stdout;
return bp;
}
int vcf_dictread(bcf_t *bp, bcf_hdr_t *h, const char *fn)
{
vcf_t *v;
gzFile fp;
kstream_t *ks;
kstring_t s, rn;
int dret;
if (bp == 0) return -1;
if (!bp->is_vcf) return 0;
s.l = s.m = 0; s.s = 0;
rn.m = rn.l = h->l_nm; rn.s = h->name;
v = (vcf_t*)bp->v;
fp = gzopen(fn, "r");
ks = ks_init(fp);
while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
bcf_str2id_add(v->refhash, strdup(s.s));
kputs(s.s, &rn); kputc('\0', &rn);
if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
}
ks_destroy(ks);
gzclose(fp);
h->l_nm = rn.l; h->name = rn.s;
bcf_hdr_sync(h);
free(s.s);
return 0;
}
int vcf_close(bcf_t *bp)
{
vcf_t *v;
if (bp == 0) return -1;
if (!bp->is_vcf) return bcf_close(bp);
v = (vcf_t*)bp->v;
if (v->fp) {
ks_destroy(v->ks);
gzclose(v->fp);
}
if (v->fpout) fclose(v->fpout);
free(v->line.s);
bcf_str2id_thorough_destroy(v->refhash);
free(v);
free(bp);
return 0;
}
int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h)
{
vcf_t *v = (vcf_t*)bp->v;
int i, has_ver = 0;
if (!bp->is_vcf) return bcf_hdr_write(bp, h);
if (h->l_txt > 0) {
if (strstr(h->txt, "##fileformat=")) has_ver = 1;
if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");
fwrite(h->txt, 1, h->l_txt - 1, v->fpout);
}
if (h->l_txt == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");
fprintf(v->fpout, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
for (i = 0; i < h->n_smpl; ++i)
fprintf(v->fpout, "\t%s", h->sns[i]);
fputc('\n', v->fpout);
return 0;
}
int vcf_write(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
{
vcf_t *v = (vcf_t*)bp->v;
extern void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s);
if (!bp->is_vcf) return bcf_write(bp, h, b);
bcf_fmt_core(h, b, &v->line);
fwrite(v->line.s, 1, v->line.l, v->fpout);
fputc('\n', v->fpout);
return v->line.l + 1;
}
int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
{
int dret, k, i, sync = 0;
vcf_t *v = (vcf_t*)bp->v;
char *p, *q;
kstring_t str, rn;
ks_tokaux_t aux, a2;
if (!bp->is_vcf) return bcf_read(bp, h, b);
v->line.l = 0;
str.l = 0; str.m = b->m_str; str.s = b->str;
rn.l = rn.m = h->l_nm; rn.s = h->name;
if (ks_getuntil(v->ks, '\n', &v->line, &dret) < 0) return -1;
b->n_smpl = h->n_smpl;
for (p = kstrtok(v->line.s, "\t", &aux), k = 0; p; p = kstrtok(0, 0, &aux), ++k) {
*(char*)aux.p = 0;
if (k == 0) { // ref
int tid = bcf_str2id(v->refhash, p);
if (tid < 0) {
tid = bcf_str2id_add(v->refhash, strdup(p));
kputs(p, &rn); kputc('\0', &rn);
sync = 1;
}
b->tid = tid;
} else if (k == 1) { // pos
b->pos = atoi(p) - 1;
} else if (k == 5) { // qual
b->qual = (p[0] >= '0' && p[0] <= '9')? atof(p) : 0;
} else if (k <= 8) { // variable length strings
kputs(p, &str); kputc('\0', &str);
b->l_str = str.l; b->m_str = str.m; b->str = str.s;
if (k == 8) bcf_sync(b);
} else { // k > 9
if (strncmp(p, "./.", 3) == 0) {
for (i = 0; i < b->n_gi; ++i) {
if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
((uint8_t*)b->gi[i].data)[k-9] = 1<<7;
} else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
((uint8_t*)b->gi[i].data)[k-9] = 0;
} else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
((int32_t*)b->gi[i].data)[k-9] = 0;
} else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
((uint16_t*)b->gi[i].data)[k-9] = 0;
} else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
int y = b->n_alleles * (b->n_alleles + 1) / 2;
memset((uint8_t*)b->gi[i].data + (k - 9) * y, 0, y);
} else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
int y = b->n_alleles * (b->n_alleles + 1) / 2;
memset((float*)b->gi[i].data + (k - 9) * y, 0, y * 4);
}
}
goto endblock;
}
for (q = kstrtok(p, ":", &a2), i = 0; q && i < b->n_gi; q = kstrtok(0, 0, &a2), ++i) {
if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
((uint8_t*)b->gi[i].data)[k-9] = (q[0] - '0')<<3 | (q[2] - '0') | (q[1] == '/'? 0 : 1) << 6;
} else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
double _x = strtod(q, &q);
int x = (int)(_x + .499);
if (x > 255) x = 255;
((uint8_t*)b->gi[i].data)[k-9] = x;
} else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
int x = strtol(q, &q, 10);
if (x > 0xffff) x = 0xffff;
((uint32_t*)b->gi[i].data)[k-9] = x;
} else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
int x = strtol(q, &q, 10);
if (x > 0xffff) x = 0xffff;
((uint16_t*)b->gi[i].data)[k-9] = x;
} else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
int x, y, j;
uint8_t *data = (uint8_t*)b->gi[i].data;
y = b->n_alleles * (b->n_alleles + 1) / 2;
for (j = 0; j < y; ++j) {
x = strtol(q, &q, 10);
if (x > 255) x = 255;
data[(k-9) * y + j] = x;
++q;
}
} else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
int j, y;
float x, *data = (float*)b->gi[i].data;
y = b->n_alleles * (b->n_alleles + 1) / 2;
for (j = 0; j < y; ++j) {
x = strtod(q, &q);
data[(k-9) * y + j] = x > 0? -x/10. : x;
++q;
}
}
}
endblock: i = i;
}
}
h->l_nm = rn.l; h->name = rn.s;
if (sync) bcf_hdr_sync(h);
return v->line.l + 1;
}
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