X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_aux.c;h=b6a8d88dcc9bde5e9f43f8e4d7f0ec1bd3ecc919;hp=d0d733fc467bfa9af7d2f032b83ffb47840ef18a;hb=9f4bebab2e0917c676ae739b2d05cb22ad6c4ed5;hpb=4a17fa7e1f91b2fe04ad334a63fc2b0d5e859d8a

diff --git a/bam_aux.c b/bam_aux.c
index d0d733f..b6a8d88 100644
--- a/bam_aux.c
+++ b/bam_aux.c
@@ -26,14 +26,12 @@ uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2])
 }
 
 #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)
+		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])
 {
@@ -115,7 +113,7 @@ int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *be
 	*ref_id = kh_value(h, iter);
 	if (i == k) { /* dump the whole sequence */
 		*begin = 0; *end = 1<<29; free(s);
-		return -1;
+		return 0;
 	}
 	for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
 	*begin = atoi(p);
@@ -181,69 +179,9 @@ char *bam_aux2Z(const uint8_t *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()
+#ifdef _WIN32
+double drand48()
 {
-	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);
+	return (double)rand() / RAND_MAX;
 }
+#endif