X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_aux.c;h=fbcd9822b233dab64f6c861fb332846acb951ce7;hb=7f8bb285b631bd30a116ff5b5495563c7f5438f2;hp=894ae628c11958dc0ed0ca49ca95d170e54ab9c7;hpb=011fa103c7af400670b23c23bea2e8c8c1391798;p=samtools.git

diff --git a/bam_aux.c b/bam_aux.c
index 894ae62..fbcd982 100644
--- a/bam_aux.c
+++ b/bam_aux.c
@@ -28,7 +28,7 @@ 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') ++(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;									\
@@ -115,7 +115,7 @@ 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);
@@ -180,70 +180,3 @@ char *bam_aux2Z(const uint8_t *s)
 	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);
-}