--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/bcftools/main.c	Fri Mar 26 16:52:45 2021 +0000
@@ -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;
+}