new file mode 100644

@@ -0,0 +1,191 @@

+#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);

+	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;

+	}

+	return 0;

+}