X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Fbcfutils.c;h=ae7ec0f0256f2bff77ad12d31f8c05ece2f518a0;hp=4d6835da8206ea96542ce66e14124b4a388e70db;hb=c34624801b980425af68c3c431423c72b18c14fe;hpb=f2f3968e11eead9ce5601b01890bc2339ff951e9

diff --git a/bcftools/bcfutils.c b/bcftools/bcfutils.c
index 4d6835d..ae7ec0f 100644
--- a/bcftools/bcfutils.c
+++ b/bcftools/bcfutils.c
@@ -1,3 +1,5 @@
+#include <string.h>
+#include <math.h>
 #include "bcf.h"
 #include "kstring.h"
 #include "khash.h"
@@ -27,6 +29,16 @@ void bcf_str2id_destroy(void *_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;
@@ -51,8 +63,9 @@ int bcf_str2id_add(void *_hash, const char *str)
 int bcf_shrink_alt(bcf1_t *b, int n)
 {
 	char *p;
-	int i, j, k, *z, n_smpl = b->n_smpl;
+	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;
@@ -61,10 +74,7 @@ int bcf_shrink_alt(bcf1_t *b, int n)
 	++p;
 	memmove(p, b->flt, b->str + b->l_str - b->flt);
 	b->l_str -= b->flt - p;
-	z = alloca(sizeof(int) / 2 * n * (n+1));
-	for (i = k = 0; i < n; ++i)
-		for (j = 0; j < n - i; ++j)
-			z[k++] = i * b->n_alleles + j;
+	// update PL
 	for (i = 0; i < b->n_gi; ++i) {
 		bcf_ginfo_t *g = b->gi + i;
 		if (g->fmt == bcf_str2int("PL", 2)) {
@@ -73,7 +83,7 @@ int bcf_shrink_alt(bcf1_t *b, int n)
 			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[z[j]];
+				for (j = 0; j < g->len; ++j) d[k++] = dl[j];
 			}
 		} // FIXME: to add GL
 	}
@@ -107,3 +117,114 @@ int bcf_gl2pl(bcf1_t *b)
 	}
 	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;
+}
+
+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;
+}
+
+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 < n; ++i)
+		k = kh_put(str2id, hash, samples[i], &ret);
+	for (i = j = 0; i < h0->n_smpl; ++i) {
+		if (kh_get(str2id, hash, h0->sns[i]) != kh_end(hash)) {
+			list[j++] = i;
+			kputs(h0->sns[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) // list MUST BE sorted
+{
+	int i, j;
+	for (j = 0; j < b->n_gi; ++j) {
+		bcf_ginfo_t *gi = b->gi + j;
+		for (i = 0; i < n_smpl; ++i)
+			memcpy((uint8_t*)gi->data + i * gi->len, (uint8_t*)gi->data + list[i] * gi->len, gi->len);
+	}
+	b->n_smpl = n_smpl;
+	return 0;
+}