#include <string.h>
#include <stdlib.h>
+#include <sys/stat.h>
+#include <unistd.h>
+#include "knetfile.h"
#include "bcf.h"
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 0x10000)
+
int bcfview(int argc, char *argv[]);
int bcf_main_index(int argc, char *argv[]);
+#define BUF_SIZE 0x10000
+
+int bcf_cat(int n, char * const *fn)
+{
+ int i;
+ bcf_t *out;
+ uint8_t *buf;
+ buf = malloc(BUF_SIZE);
+ out = bcf_open("-", "w");
+ for (i = 0; i < n; ++i) {
+ bcf_t *in;
+ bcf_hdr_t *h;
+ off_t end;
+ struct stat s;
+ in = bcf_open(fn[i], "r");
+ h = bcf_hdr_read(in);
+ if (i == 0) bcf_hdr_write(out, h);
+ bcf_hdr_destroy(h);
+#ifdef _USE_KNETFILE
+ fstat(knet_fileno((knetFile*)in->fp->fp), &s);
+ end = s.st_size - 28;
+ while (knet_tell((knetFile*)in->fp->fp) < end) {
+ int size = knet_tell((knetFile*)in->fp->fp) + BUF_SIZE < end? BUF_SIZE : end - knet_tell((knetFile*)in->fp->fp);
+ knet_read(in->fp->fp, buf, size);
+ fwrite(buf, 1, size, out->fp->fp);
+ }
+#else
+ abort(); // FIXME: not implemented
+#endif
+ bcf_close(in);
+ }
+ bcf_close(out);
+ free(buf);
+ return 0;
+}
+
+extern double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]);
+
+int bcf_main_ldpair(int argc, char *argv[])
+{
+ bcf_t *fp;
+ bcf_hdr_t *h;
+ bcf1_t *b0, *b1;
+ bcf_idx_t *idx;
+ kstring_t str;
+ void *str2id;
+ gzFile fplist;
+ kstream_t *ks;
+ int dret, lineno = 0;
+ if (argc < 3) {
+ fprintf(stderr, "Usage: bcftools ldpair <in.bcf> <in.list>\n");
+ return 1;
+ }
+ fplist = gzopen(argv[2], "rb");
+ ks = ks_init(fplist);
+ memset(&str, 0, sizeof(kstring_t));
+ fp = bcf_open(argv[1], "rb");
+ h = bcf_hdr_read(fp);
+ str2id = bcf_build_refhash(h);
+ idx = bcf_idx_load(argv[1]);
+ if (idx == 0) {
+ fprintf(stderr, "[%s] No bcf index is found. Abort!\n", __func__);
+ return 1;
+ }
+ b0 = calloc(1, sizeof(bcf1_t));
+ b1 = calloc(1, sizeof(bcf1_t));
+ while (ks_getuntil(ks, '\n', &str, &dret) >= 0) {
+ char *p, *q;
+ int k;
+ int tid0 = -1, tid1 = -1, pos0 = -1, pos1 = -1;
+ ++lineno;
+ for (p = q = str.s, k = 0; *p; ++p) {
+ if (*p == ' ' || *p == '\t') {
+ *p = '\0';
+ if (k == 0) tid0 = bcf_str2id(str2id, q);
+ else if (k == 1) pos0 = atoi(q) - 1;
+ else if (k == 2) tid1 = strcmp(q, "=")? bcf_str2id(str2id, q) : tid0;
+ else if (k == 3) pos1 = atoi(q) - 1;
+ q = p + 1;
+ ++k;
+ }
+ }
+ if (k == 3) pos1 = atoi(q) - 1;
+ if (tid0 >= 0 && tid1 >= 0 && pos0 >= 0 && pos1 >= 0) {
+ uint64_t off;
+ double r, f[4];
+ off = bcf_idx_query(idx, tid0, pos0);
+ bgzf_seek(fp->fp, off, SEEK_SET);
+ while (bcf_read(fp, h, b0) >= 0 && b0->pos != pos0);
+ off = bcf_idx_query(idx, tid1, pos1);
+ bgzf_seek(fp->fp, off, SEEK_SET);
+ while (bcf_read(fp, h, b1) >= 0 && b1->pos != pos1);
+ r = bcf_pair_freq(b0, b1, f);
+ r *= r;
+ printf("%s\t%d\t%s\t%d\t%.4g\t%.4g\t%.4g\t%.4g\t%.4g\n", h->ns[tid0], pos0+1, h->ns[tid1], pos1+1,
+ r, f[0], f[1], f[2], f[3]);
+ } //else fprintf(stderr, "[%s] Parse error at line %d.\n", __func__, lineno);
+ }
+ bcf_destroy(b0); bcf_destroy(b1);
+ bcf_idx_destroy(idx);
+ bcf_str2id_destroy(str2id);
+ bcf_hdr_destroy(h);
+ bcf_close(fp);
+ free(str.s);
+ ks_destroy(ks);
+ gzclose(fplist);
+ return 0;
+}
+
+int bcf_main_ld(int argc, char *argv[])
+{
+ bcf_t *fp;
+ bcf_hdr_t *h;
+ bcf1_t **b, *b0;
+ int i, j, m, n;
+ double f[4];
+ if (argc == 1) {
+ fprintf(stderr, "Usage: bcftools ld <in.bcf>\n");
+ return 1;
+ }
+ fp = bcf_open(argv[1], "rb");
+ h = bcf_hdr_read(fp);
+ // read the entire BCF
+ m = n = 0; b = 0;
+ b0 = calloc(1, sizeof(bcf1_t));
+ while (bcf_read(fp, h, b0) >= 0) {
+ if (m == n) {
+ m = m? m<<1 : 16;
+ b = realloc(b, sizeof(void*) * m);
+ }
+ b[n] = calloc(1, sizeof(bcf1_t));
+ bcf_cpy(b[n++], b0);
+ }
+ bcf_destroy(b0);
+ // compute pair-wise r^2
+ printf("%d\n", n); // the number of loci
+ for (i = 0; i < n; ++i) {
+ printf("%s:%d", h->ns[b[i]->tid], b[i]->pos + 1);
+ for (j = 0; j < i; ++j) {
+ double r = bcf_pair_freq(b[i], b[j], f);
+ printf("\t%.3f", r*r);
+ }
+ printf("\t1.000\n");
+ }
+ // free
+ for (i = 0; i < n; ++i) bcf_destroy(b[i]);
+ free(b);
+ bcf_hdr_destroy(h);
+ bcf_close(fp);
+ return 0;
+}
+
int main(int argc, char *argv[])
{
if (argc == 1) {
fprintf(stderr, "\n");
+ fprintf(stderr, "Program: bcftools (Tools for data in the VCF/BCF formats)\n");
+ fprintf(stderr, "Version: %s\n\n", BCF_VERSION);
fprintf(stderr, "Usage: bcftools <command> <arguments>\n\n");
fprintf(stderr, "Command: view print, extract, convert and call SNPs from BCF\n");
fprintf(stderr, " index index BCF\n");
+ fprintf(stderr, " cat concatenate BCFs\n");
+ fprintf(stderr, " ld compute all-pair r^2\n");
+ fprintf(stderr, " ldpair compute r^2 between requested pairs\n");
fprintf(stderr, "\n");
return 1;
}
if (strcmp(argv[1], "view") == 0) return bcfview(argc-1, argv+1);
- if (strcmp(argv[1], "index") == 0) return bcf_main_index(argc-1, argv+1);
- if (strcmp(argv[1], "test") == 0) return vcf_test(argc-1, argv+1);
+ else if (strcmp(argv[1], "index") == 0) return bcf_main_index(argc-1, argv+1);
+ else if (strcmp(argv[1], "ld") == 0) return bcf_main_ld(argc-1, argv+1);
+ else if (strcmp(argv[1], "ldpair") == 0) return bcf_main_ldpair(argc-1, argv+1);
+ else if (strcmp(argv[1], "cat") == 0) return bcf_cat(argc-2, argv+2); // cat is different ...
else {
fprintf(stderr, "[main] Unrecognized command.\n");
return 1;