+#include <string.h>
+#include <ctype.h>
+#include <stdio.h>
+#include "kstring.h"
+#include "bcf.h"
+
+int bcf_hdr_read(bcf_t *b);
+
+void bcf_hdr_clear(bcf_hdr_t *b)
+{
+ free(b->name); free(b->sname); free(b->txt); free(b->ns); free(b->sns);
+ memset(b, 0, sizeof(bcf_hdr_t));
+}
+
+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), "w");
+ } else {
+ b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdin), "r");
+ }
+ b->fp->owned_file = 1;
+ if (strchr(mode, 'r')) bcf_hdr_read(b);
+ return b;
+}
+
+int bcf_close(bcf_t *b)
+{
+ int ret;
+ if (b == 0) return 0;
+ ret = bgzf_close(b->fp);
+ free(b->h.name); free(b->h.sname); free(b->h.txt); free(b->h.ns); free(b->h.sns);
+ free(b);
+ return ret;
+}
+
+int bcf_hdr_write(bcf_t *b)
+{
+ bcf_hdr_t *h;
+ if (b == 0) return -1;
+ h = &b->h;
+ 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;
+}
+
+int bcf_hdr_read(bcf_t *b)
+{
+ uint8_t magic[4];
+ bcf_hdr_t *h;
+ if (b == 0) return -1;
+ bcf_hdr_clear(&b->h);
+ h = &b->h;
+ 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(&b->h);
+ return 16 + h->l_nm + h->l_smpl + h->l_txt;
+}
+
+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;
+ b->ns = cnt_null(b->l_nm, b->name, &b->n_ref);
+ b->sns = cnt_null(b->l_smpl, b->sname, &b->n_smpl);
+ return 0;
+}
+
+#define char2int(s) (((int)s[0])<<8|s[1])
+
+int bcf_sync(int n_smpl, bcf1_t *b)
+{
+ char *p, *tmp[4], *s;
+ int i, n, c;
+ // 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) tmp[n++] = p + 1;
+ if (n != 5) 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
+ for (p = b->alt, n = 1; *p; ++p)
+ if (*p == ',') ++n;
+ b->n_alleles = n;
+ c = toupper(*b->ref);
+ if (b->alt - b->ref == 2 && (c == 'A' || c == 'C' || c == 'G' || c == 'T'))
+ ++b->n_alleles;
+ // 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 = s = b->fmt, n = 0; *p; ++p) {
+ if (*p == ':' || *(p+1) == 0) {
+ char *q = *p == ':'? p : p + 1;
+ if ((q - s) != 2) return -2;
+ b->gi[n].fmt = char2int(s);
+ s = q;
+ }
+ }
+ // set gi[i].len
+ for (i = 0; i < b->n_gi; ++i) {
+ if (b->gi[i].fmt == char2int("PL")) {
+ b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2;
+ } else if (b->gi[i].fmt == char2int("DP") || b->gi[i].fmt == char2int("HQ")) {
+ b->gi[i].len = 2;
+ } else if (b->gi[i].fmt == char2int("GQ") || b->gi[i].fmt == char2int("GT")) {
+ b->gi[i].len = 1;
+ } else if (b->gi[i].fmt == char2int("GL")) {
+ b->gi[i].len = 4;
+ }
+ b->gi[i].data = malloc(n_smpl * b->gi[i].len);
+ }
+ return 0;
+}
+
+int bcf_write(bcf_t *bp, const bcf1_t *b)
+{
+ uint32_t x;
+ int i, l = 0;
+ if (b == 0) return -1;
+ bgzf_write(bp->fp, &b->tid, 4);
+ bgzf_write(bp->fp, &b->pos, 4);
+ x = b->qual<<24 | b->l_str;
+ bgzf_write(bp->fp, &x, 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 * bp->h.n_smpl);
+ l += b->gi[i].len * bp->h.n_smpl;
+ }
+ return l;
+}
+
+int bcf_read(bcf_t *bp, bcf1_t *b)
+{
+ int i, l = 0;
+ uint32_t x;
+ if (b == 0) return -1;
+ if (bgzf_read(bp->fp, &b->tid, 4) == 0) return 0;
+ bgzf_read(bp->fp, &b->pos, 4);
+ bgzf_read(bp->fp, &x, 4);
+ b->qual = x >> 24; b->l_str = x << 8 >> 8;
+ 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;
+ bcf_sync(bp->h.n_smpl, b);
+ for (i = 0; i < b->n_gi; ++i) {
+ bgzf_read(bp->fp, b->gi[i].data, b->gi[i].len * bp->h.n_smpl);
+ l += b->gi[i].len * bp->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->n_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);
+}
+
+char *bcf_fmt(bcf_t *bp, bcf1_t *b)
+{
+ kstring_t s;
+ int i, j, x;
+ memset(&s, 0, sizeof(kstring_t));
+ kputs(bp->h.ns[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);
+ kputw(b->qual, &s); kputc('\t', &s);
+ fmt_str(b->info, &s); kputc('\t', &s);
+ fmt_str(b->fmt, &s);
+ x = b->n_alleles * (b->n_alleles + 1) / 2;
+ for (j = 0; j < bp->h.n_smpl; ++j) {
+ kputc('\t', &s);
+ for (i = 0; i < b->n_gi; ++i) {
+ if (i) kputc(':', &s);
+ if (b->gi[i].fmt == char2int("PL")) {
+ uint8_t *d = (uint8_t*)b->gi[i].data + j * x;
+ int k;
+ for (k = 0; k < x; ++k) {
+ if (k > 0) kputc(',', &s);
+ kputw(d[k], &s);
+ }
+ } else if (b->gi[i].fmt == char2int("DP")) {
+ kputw(((uint16_t*)b->gi[i].data)[j], &s);
+ } else if (b->gi[i].fmt == char2int("GQ")) {
+ kputw(((uint8_t*)b->gi[i].data)[j], &s);
+ }
+ }
+ }
+ return s.s;
+}