diff SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/bam_aux.c @ 0:74f5ea818cea

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/bam_aux.c	Wed Oct 12 19:50:38 2011 -0400
@@ -0,0 +1,249 @@
+#include <ctype.h>
+#include "bam.h"
+#include "khash.h"
+typedef char *str_p;
+KHASH_MAP_INIT_STR(s, int)
+KHASH_MAP_INIT_STR(r2l, str_p)
+
+void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data)
+{
+	int ori_len = b->data_len;
+	b->data_len += 3 + len;
+	b->l_aux += 3 + len;
+	if (b->m_data < b->data_len) {
+		b->m_data = b->data_len;
+		kroundup32(b->m_data);
+		b->data = (uint8_t*)realloc(b->data, b->m_data);
+	}
+	b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1];
+	b->data[ori_len + 2] = type;
+	memcpy(b->data + ori_len + 3, data, len);
+}
+
+uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2])
+{
+	return bam_aux_get(b, tag);
+}
+
+#define __skip_tag(s) do { \
+		int type = toupper(*(s));										\
+		++(s);															\
+		if (type == 'C' || type == 'A') ++(s);							\
+		else if (type == 'S') (s) += 2;									\
+		else if (type == 'I' || type == 'F') (s) += 4;					\
+		else if (type == 'D') (s) += 8;									\
+		else if (type == 'Z' || type == 'H') { while (*(s)) ++(s); ++(s); } \
+	} while (0)
+
+uint8_t *bam_aux_get(const bam1_t *b, const char tag[2])
+{
+	uint8_t *s;
+	int y = tag[0]<<8 | tag[1];
+	s = bam1_aux(b);
+	while (s < b->data + b->data_len) {
+		int x = (int)s[0]<<8 | s[1];
+		s += 2;
+		if (x == y) return s;
+		__skip_tag(s);
+	}
+	return 0;
+}
+// s MUST BE returned by bam_aux_get()
+int bam_aux_del(bam1_t *b, uint8_t *s)
+{
+	uint8_t *p, *aux;
+	aux = bam1_aux(b);
+	p = s - 2;
+	__skip_tag(s);
+	memmove(p, s, b->l_aux - (s - aux));
+	b->data_len -= s - p;
+	b->l_aux -= s - p;
+	return 0;
+}
+
+void bam_init_header_hash(bam_header_t *header)
+{
+	if (header->hash == 0) {
+		int ret, i;
+		khiter_t iter;
+		khash_t(s) *h;
+		header->hash = h = kh_init(s);
+		for (i = 0; i < header->n_targets; ++i) {
+			iter = kh_put(s, h, header->target_name[i], &ret);
+			kh_value(h, iter) = i;
+		}
+	}
+}
+
+void bam_destroy_header_hash(bam_header_t *header)
+{
+	if (header->hash)
+		kh_destroy(s, (khash_t(s)*)header->hash);
+}
+
+int32_t bam_get_tid(const bam_header_t *header, const char *seq_name)
+{
+	khint_t k;
+	khash_t(s) *h = (khash_t(s)*)header->hash;
+	k = kh_get(s, h, seq_name);
+	return k == kh_end(h)? -1 : kh_value(h, k);
+}
+
+int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end)
+{
+	char *s, *p;
+	int i, l, k;
+	khiter_t iter;
+	khash_t(s) *h;
+
+	bam_init_header_hash(header);
+	h = (khash_t(s)*)header->hash;
+
+	l = strlen(str);
+	p = s = (char*)malloc(l+1);
+	/* squeeze out "," */
+	for (i = k = 0; i != l; ++i)
+		if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
+	s[k] = 0;
+	for (i = 0; i != k; ++i) if (s[i] == ':') break;
+	s[i] = 0;
+	iter = kh_get(s, h, s); /* get the ref_id */
+	if (iter == kh_end(h)) { // name not found
+		*ref_id = -1; free(s);
+		return -1;
+	}
+	*ref_id = kh_value(h, iter);
+	if (i == k) { /* dump the whole sequence */
+		*begin = 0; *end = 1<<29; free(s);
+		return -1;
+	}
+	for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
+	*begin = atoi(p);
+	if (i < k) {
+		p = s + i + 1;
+		*end = atoi(p);
+	} else *end = 1<<29;
+	if (*begin > 0) --*begin;
+	free(s);
+	if (*begin > *end) {
+		fprintf(stderr, "[bam_parse_region] invalid region.\n");
+		return -1;
+	}
+	return 0;
+}
+
+int32_t bam_aux2i(const uint8_t *s)
+{
+	int type;
+	if (s == 0) return 0;
+	type = *s++;
+	if (type == 'c') return (int32_t)*(int8_t*)s;
+	else if (type == 'C') return (int32_t)*(uint8_t*)s;
+	else if (type == 's') return (int32_t)*(int16_t*)s;
+	else if (type == 'S') return (int32_t)*(uint16_t*)s;
+	else if (type == 'i' || type == 'I') return *(int32_t*)s;
+	else return 0;
+}
+
+float bam_aux2f(const uint8_t *s)
+{
+	int type;
+	type = *s++;
+	if (s == 0) return 0.0;
+	if (type == 'f') return *(float*)s;
+	else return 0.0;
+}
+
+double bam_aux2d(const uint8_t *s)
+{
+	int type;
+	type = *s++;
+	if (s == 0) return 0.0;
+	if (type == 'd') return *(double*)s;
+	else return 0.0;
+}
+
+char bam_aux2A(const uint8_t *s)
+{
+	int type;
+	type = *s++;
+	if (s == 0) return 0;
+	if (type == 'A') return *(char*)s;
+	else return 0;
+}
+
+char *bam_aux2Z(const uint8_t *s)
+{
+	int type;
+	type = *s++;
+	if (s == 0) return 0;
+	if (type == 'Z' || type == 'H') return (char*)s;
+	else return 0;
+}
+
+/******************
+ * rg2lib related *
+ ******************/
+
+int bam_strmap_put(void *rg2lib, const char *rg, const char *lib)
+{
+	int ret;
+	khint_t k;
+	khash_t(r2l) *h = (khash_t(r2l)*)rg2lib;
+	char *key;
+	if (h == 0) return 1;
+	key = strdup(rg);
+	k = kh_put(r2l, h, key, &ret);
+	if (ret) kh_val(h, k) = strdup(lib);
+	else {
+		fprintf(stderr, "[bam_rg2lib_put] duplicated @RG ID: %s\n", rg);
+		free(key);
+	}
+	return 0;
+}
+
+const char *bam_strmap_get(const void *rg2lib, const char *rg)
+{
+	const khash_t(r2l) *h = (const khash_t(r2l)*)rg2lib;
+	khint_t k;
+	if (h == 0) return 0;
+	k = kh_get(r2l, h, rg);
+	if (k != kh_end(h)) return (const char*)kh_val(h, k);
+	else return 0;
+}
+
+void *bam_strmap_dup(const void *rg2lib)
+{
+	const khash_t(r2l) *h = (const khash_t(r2l)*)rg2lib;
+	khash_t(r2l) *g;
+	khint_t k, l;
+	int ret;
+	if (h == 0) return 0;
+	g = kh_init(r2l);
+	for (k = kh_begin(h); k < kh_end(h); ++k) {
+		if (kh_exist(h, k)) {
+			char *key = strdup(kh_key(h, k));
+			l = kh_put(r2l, g, key, &ret);
+			kh_val(g, l) = strdup(kh_val(h, k));
+		}
+	}
+	return g;
+}
+
+void *bam_strmap_init()
+{
+	return (void*)kh_init(r2l);
+}
+
+void bam_strmap_destroy(void *rg2lib)
+{
+	khash_t(r2l) *h = (khash_t(r2l)*)rg2lib;
+	khint_t k;
+	if (h == 0) return;
+	for (k = kh_begin(h); k < kh_end(h); ++k) {
+		if (kh_exist(h, k)) {
+			free((char*)kh_key(h, k)); free(kh_val(h, k));
+		}
+	}
+	kh_destroy(r2l, h);
+}