X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fbam_aux.c;fp=samtools%2Fbam_aux.c;h=0000000000000000000000000000000000000000;hp=fbcd9822b233dab64f6c861fb332846acb951ce7;hb=d02fe5283ed7a93a2f76a5d6dc6e37b40c11b9b1;hpb=d828f9c9aa78e3d1687265b52de841f3f3852089

diff --git a/samtools/bam_aux.c b/samtools/bam_aux.c
deleted file mode 100644
index fbcd982..0000000
--- a/samtools/bam_aux.c
+++ /dev/null
@@ -1,182 +0,0 @@
-#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 0;
-	}
-	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;
-}