new file mode 100644

@@ -0,0 +1,217 @@

+#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 == 'Z' || type == 'H') { while (*(s)) ++(s); ++(s); } \

+		else if (type == 'B') (s) += 5 + bam_aux_type2size(*(s)) * (*(int32_t*)((s)+1)); \

+		else (s) += bam_aux_type2size(type); \

+	} 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;

+}

+

+int bam_aux_drop_other(bam1_t *b, uint8_t *s)

+{

+	if (s) {

+		uint8_t *p, *aux;

+		aux = bam1_aux(b);

+		p = s - 2;

+		__skip_tag(s);

+		memmove(aux, p, s - p);

+		b->data_len -= b->l_aux - (s - p);

+		b->l_aux = s - p;

+	} else {

+		b->data_len -= b->l_aux;

+		b->l_aux = 0;

+	}

+	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 *beg, int *end)

+{

+	char *s;

+	int i, l, k, name_end;

+	khiter_t iter;

+	khash_t(s) *h;

+

+	bam_init_header_hash(header);

+	h = (khash_t(s)*)header->hash;

+

+	*ref_id = *beg = *end = -1;

+	name_end = l = strlen(str);

+	s = (char*)malloc(l+1);

+	// remove space

+	for (i = k = 0; i < l; ++i)

+		if (!isspace(str[i])) s[k++] = str[i];

+	s[k] = 0; l = k;

+	// determine the sequence name

+	for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end

+	if (i >= 0) name_end = i;

+	if (name_end < l) { // check if this is really the end

+		int n_hyphen = 0;

+		for (i = name_end + 1; i < l; ++i) {

+			if (s[i] == '-') ++n_hyphen;

+			else if (!isdigit(s[i]) && s[i] != ',') break;

+		}

+		if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name

+		s[name_end] = 0;

+		iter = kh_get(s, h, s);

+		if (iter == kh_end(h)) { // cannot find the sequence name

+			iter = kh_get(s, h, str); // try str as the name

+			if (iter == kh_end(h)) {

+				if (bam_verbose >= 2) fprintf(stderr, "[%s] fail to determine the sequence name.\n", __func__);

+				free(s); return -1;

+			} else s[name_end] = ':', name_end = l;

+		}

+	} else iter = kh_get(s, h, str);

+        if (iter == kh_end(h)) {

+          free(s); 

+          return -1;

+        }

+	*ref_id = kh_val(h, iter);

+	// parse the interval

+	if (name_end < l) {

+		for (i = k = name_end + 1; i < l; ++i)

+			if (s[i] != ',') s[k++] = s[i];

+		s[k] = 0;

+		*beg = atoi(s + name_end + 1);

+		for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break;

+		*end = i < k? atoi(s + i + 1) : 1<<29;

+		if (*beg > 0) --*beg;

+	} else *beg = 0, *end = 1<<29;

+	free(s);

+	return *beg <= *end? 0 : -1;

+}

+

+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;

+}

+

+#ifdef _WIN32

+double drand48()

+{

+	return (double)rand() / RAND_MAX;

+}

+#endif