X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Fld.c;fp=bcftools%2Fld.c;h=0207819bc731762b30908cef687b35134cee0f65;hp=11474ed422aa40e5b839831a5c0b5ab80f5c73ad;hb=e42445c748ed193f8d0a4277a844fa848f30c132;hpb=fa217aa47313e2535cbd2d4bb034cfd405162662

diff --git a/bcftools/ld.c b/bcftools/ld.c
index 11474ed..0207819 100644
--- a/bcftools/ld.c
+++ b/bcftools/ld.c
@@ -98,3 +98,46 @@ double bcf_ld_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4])
 	}
 	return r;
 }
+
+int bcf_main_pwld(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 pwld <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_ld_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;
+}