--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/samtools-0.1.16/bcftools/bcfutils.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,310 @@
+#include <string.h>
+#include <math.h>
+#include "bcf.h"
+#include "kstring.h"
+#include "khash.h"
+KHASH_MAP_INIT_STR(str2id, int)
+
+void *bcf_build_refhash(bcf_hdr_t *h)
+{
+	khash_t(str2id) *hash;
+	int i, ret;
+	hash = kh_init(str2id);
+	for (i = 0; i < h->n_ref; ++i) {
+		khint_t k;
+		k = kh_put(str2id, hash, h->ns[i], &ret); // FIXME: check ret
+		kh_val(hash, k) = i;
+	}
+	return hash;
+}
+
+void *bcf_str2id_init()
+{
+	return kh_init(str2id);
+}
+
+void bcf_str2id_destroy(void *_hash)
+{
+	khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
+	if (hash) kh_destroy(str2id, hash); // Note that strings are not freed.
+}
+
+void bcf_str2id_thorough_destroy(void *_hash)
+{
+	khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
+	khint_t k;
+	if (hash == 0) return;
+	for (k = 0; k < kh_end(hash); ++k)
+		if (kh_exist(hash, k)) free((char*)kh_key(hash, k));
+	kh_destroy(str2id, hash);
+}
+
+int bcf_str2id(void *_hash, const char *str)
+{
+	khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
+	khint_t k;
+	if (!hash) return -1;
+	k = kh_get(str2id, hash, str);
+	return k == kh_end(hash)? -1 : kh_val(hash, k);
+}
+
+int bcf_str2id_add(void *_hash, const char *str)
+{
+	khint_t k;
+	int ret;
+	khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
+	if (!hash) return -1;
+	k = kh_put(str2id, hash, str, &ret);
+	if (ret == 0) return kh_val(hash, k);
+	kh_val(hash, k) = kh_size(hash) - 1;
+	return kh_val(hash, k);
+}
+
+int bcf_shrink_alt(bcf1_t *b, int n)
+{
+	char *p;
+	int i, j, k, n_smpl = b->n_smpl;
+	if (b->n_alleles <= n) return -1;
+	// update ALT
+	if (n > 1) {
+		for (p = b->alt, k = 1; *p; ++p)
+			if (*p == ',' && ++k == n) break;
+		*p = '\0';
+	} else p = b->alt, *p = '\0';
+	++p;
+	memmove(p, b->flt, b->str + b->l_str - b->flt);
+	b->l_str -= b->flt - p;
+	// update PL
+	for (i = 0; i < b->n_gi; ++i) {
+		bcf_ginfo_t *g = b->gi + i;
+		if (g->fmt == bcf_str2int("PL", 2)) {
+			int l, x = b->n_alleles * (b->n_alleles + 1) / 2;
+			uint8_t *d = (uint8_t*)g->data;
+			g->len = n * (n + 1) / 2;
+			for (l = k = 0; l < n_smpl; ++l) {
+				uint8_t *dl = d + l * x;
+				for (j = 0; j < g->len; ++j) d[k++] = dl[j];
+			}
+		} // FIXME: to add GL
+	}
+	b->n_alleles = n;
+	bcf_sync(b);
+	return 0;
+}
+
+int bcf_gl2pl(bcf1_t *b)
+{
+	char *p;
+	int i, n_smpl = b->n_smpl;
+	bcf_ginfo_t *g;
+	float *d0;
+	uint8_t *d1;
+	if (strstr(b->fmt, "PL")) return -1;
+	if ((p = strstr(b->fmt, "GL")) == 0) return -1;
+	*p = 'P';
+	for (i = 0; i < b->n_gi; ++i)
+		if (b->gi[i].fmt == bcf_str2int("GL", 2))
+			break;
+	g = b->gi + i;
+	g->fmt = bcf_str2int("PL", 2);
+	g->len /= 4; // 4 == sizeof(float)
+	d0 = (float*)g->data; d1 = (uint8_t*)g->data;
+	for (i = 0; i < n_smpl * g->len; ++i) {
+		int x = (int)(-10. * d0[i] + .499);
+		if (x > 255) x = 255;
+		if (x < 0) x = 0;
+		d1[i] = x;
+	}
+	return 0;
+}
+/* FIXME: this function will fail given AB:GTX:GT. BCFtools never
+ * produces such FMT, but others may do. */
+int bcf_fix_gt(bcf1_t *b)
+{
+	char *s;
+	int i;
+	uint32_t tmp;
+	bcf_ginfo_t gt;
+	// check the presence of the GT FMT
+	if ((s = strstr(b->fmt, ":GT")) == 0) return 0; // no GT or GT is already the first
+	if (s[3] != '\0' && s[3] != ':') return 0; // :GTX in fact
+	tmp = bcf_str2int("GT", 2);
+	for (i = 0; i < b->n_gi; ++i)
+		if (b->gi[i].fmt == tmp) break;
+	if (i == b->n_gi) return 0; // no GT in b->gi; probably a bug...
+	gt = b->gi[i];
+	// move GT to the first
+	for (; i > 0; --i) b->gi[i] = b->gi[i-1];
+	b->gi[0] = gt;
+	memmove(b->fmt + 3, b->fmt, s + 1 - b->fmt);
+	b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':';
+	return 0;
+}
+
+int bcf_fix_pl(bcf1_t *b)
+{
+	int i;
+	uint32_t tmp;
+	uint8_t *PL, *swap;
+	bcf_ginfo_t *gi;
+	// pinpoint PL
+	tmp = bcf_str2int("PL", 2);
+	for (i = 0; i < b->n_gi; ++i)
+		if (b->gi[i].fmt == tmp) break;
+	if (i == b->n_gi) return 0;
+	// prepare
+	gi = b->gi + i;
+	PL = (uint8_t*)gi->data;
+	swap = alloca(gi->len);
+	// loop through individuals
+	for (i = 0; i < b->n_smpl; ++i) {
+		int k, l, x;
+		uint8_t *PLi = PL + i * gi->len;
+		memcpy(swap, PLi, gi->len);
+		for (k = x = 0; k < b->n_alleles; ++k)
+			for (l = k; l < b->n_alleles; ++l)
+				PLi[l*(l+1)/2 + k] = swap[x++];
+	}
+	return 0;
+}
+
+int bcf_smpl_covered(const bcf1_t *b)
+{
+	int i, j, n = 0;
+	uint32_t tmp;
+	bcf_ginfo_t *gi;
+	// pinpoint PL
+	tmp = bcf_str2int("PL", 2);
+	for (i = 0; i < b->n_gi; ++i)
+		if (b->gi[i].fmt == tmp) break;
+	if (i == b->n_gi) return 0;
+	// count how many samples having PL!=[0..0]
+	gi = b->gi + i;
+	for (i = 0; i < b->n_smpl; ++i) {
+		uint8_t *PLi = ((uint8_t*)gi->data) + i * gi->len;
+		for (j = 0; j < gi->len; ++j)
+			if (PLi[j]) break;
+		if (j < gi->len) ++n;
+	}
+	return n;
+}
+
+static void *locate_field(const bcf1_t *b, const char *fmt, int l)
+{
+	int i;
+	uint32_t tmp;
+	tmp = bcf_str2int(fmt, l);
+	for (i = 0; i < b->n_gi; ++i)
+		if (b->gi[i].fmt == tmp) break;
+	return i == b->n_gi? 0 : b->gi[i].data;
+}
+
+int bcf_anno_max(bcf1_t *b)
+{
+	int k, max_gq, max_sp, n_het;
+	kstring_t str;
+	uint8_t *gt, *gq;
+	int32_t *sp;
+	max_gq = max_sp = n_het = 0;
+	gt = locate_field(b, "GT", 2);
+	if (gt == 0) return -1;
+	gq = locate_field(b, "GQ", 2);
+	sp = locate_field(b, "SP", 2);
+	if (sp)
+		for (k = 0; k < b->n_smpl; ++k)
+			if (gt[k]&0x3f)
+				max_sp = max_sp > (int)sp[k]? max_sp : sp[k];
+	if (gq)
+		for (k = 0; k < b->n_smpl; ++k)
+			if (gt[k]&0x3f)
+				max_gq = max_gq > (int)gq[k]? max_gq : gq[k];
+	for (k = 0; k < b->n_smpl; ++k) {
+		int a1, a2;
+		a1 = gt[k]&7; a2 = gt[k]>>3&7;
+		if ((!a1 && a2) || (!a2 && a1)) { // a het
+			if (gq == 0) ++n_het;
+			else if (gq[k] >= 20) ++n_het;
+		}
+	}
+	if (n_het) max_sp -= (int)(4.343 * log(n_het) + .499);
+	if (max_sp < 0) max_sp = 0;
+	memset(&str, 0, sizeof(kstring_t));
+	if (*b->info) kputc(';', &str);
+	ksprintf(&str, "MXSP=%d;MXGQ=%d", max_sp, max_gq);
+	bcf_append_info(b, str.s, str.l);
+	free(str.s);
+	return 0;
+}
+
+// FIXME: only data are shuffled; the header is NOT
+int bcf_shuffle(bcf1_t *b, int seed)
+{
+	int i, j, *a;
+	if (seed > 0) srand48(seed);
+	a = malloc(b->n_smpl * sizeof(int));
+	for (i = 0; i < b->n_smpl; ++i) a[i] = i;
+	for (i = b->n_smpl; i > 1; --i) {
+		int tmp;
+		j = (int)(drand48() * i);
+		tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp;
+	}
+	for (j = 0; j < b->n_gi; ++j) {
+		bcf_ginfo_t *gi = b->gi + j;
+		uint8_t *swap, *data = (uint8_t*)gi->data;
+		swap = malloc(gi->len * b->n_smpl);
+		for (i = 0; i < b->n_smpl; ++i)
+			memcpy(swap + gi->len * a[i], data + gi->len * i, gi->len);
+		free(gi->data);
+		gi->data = swap;
+	}
+	free(a);
+	return 0;
+}
+
+bcf_hdr_t *bcf_hdr_subsam(const bcf_hdr_t *h0, int n, char *const* samples, int *list)
+{
+	int i, ret, j;
+	khint_t k;
+	bcf_hdr_t *h;
+	khash_t(str2id) *hash;
+	kstring_t s;
+	s.l = s.m = 0; s.s = 0;
+	hash = kh_init(str2id);
+	for (i = 0; i < h0->n_smpl; ++i) {
+		k = kh_put(str2id, hash, h0->sns[i], &ret);
+		kh_val(hash, k) = i;
+	}
+	for (i = j = 0; i < n; ++i) {
+		k = kh_get(str2id, hash, samples[i]);
+		if (k != kh_end(hash)) {
+			list[j++] = kh_val(hash, k);
+			kputs(samples[i], &s); kputc('\0', &s);
+		}
+	}
+	if (j < n) fprintf(stderr, "<%s> %d samples in the list but not in BCF.", __func__, n - j);
+	kh_destroy(str2id, hash);
+	h = calloc(1, sizeof(bcf_hdr_t));
+	*h = *h0;
+	h->ns = 0; h->sns = 0;
+	h->name = malloc(h->l_nm); memcpy(h->name, h0->name, h->l_nm);
+	h->txt = calloc(1, h->l_txt + 1); memcpy(h->txt, h0->txt, h->l_txt);
+	h->l_smpl = s.l; h->sname = s.s;
+	bcf_hdr_sync(h);
+	return h;
+}
+
+int bcf_subsam(int n_smpl, int *list, bcf1_t *b)
+{
+	int i, j;
+	for (j = 0; j < b->n_gi; ++j) {
+		bcf_ginfo_t *gi = b->gi + j;
+		uint8_t *swap;
+		swap = malloc(gi->len * b->n_smpl);
+		for (i = 0; i < n_smpl; ++i)
+			memcpy(swap + i * gi->len, (uint8_t*)gi->data + list[i] * gi->len, gi->len);
+		free(gi->data);
+		gi->data = swap;
+	}
+	b->n_smpl = n_smpl;
+	return 0;
+}