X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_aux.c;h=28b22e3059273da57dd8395fba5e29287dc3228b;hp=fbcd9822b233dab64f6c861fb332846acb951ce7;hb=9a36c994ed991f79cc191ece6cbc5f1bf6410da2;hpb=67801bf17aa6495879da63ce77a2014759fabc16

diff --git a/bam_aux.c b/bam_aux.c
index fbcd982..28b22e3 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])
 {
@@ -61,6 +59,23 @@ int bam_aux_del(bam1_t *b, uint8_t *s)
 	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) {
@@ -89,47 +104,56 @@ int32_t bam_get_tid(const bam_header_t *header, const char *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)
+int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *beg, int *end)
 {
-	char *s, *p;
-	int i, l, k;
+	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;
 
-	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;
+	*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);
+	*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);
-	if (*begin > *end) {
-		fprintf(stderr, "[bam_parse_region] invalid region.\n");
-		return -1;
-	}
-	return 0;
+	return *beg <= *end? 0 : -1;
 }
 
 int32_t bam_aux2i(const uint8_t *s)
@@ -180,3 +204,10 @@ char *bam_aux2Z(const uint8_t *s)
 	if (type == 'Z' || type == 'H') return (char*)s;
 	else return 0;
 }
+
+#ifdef _WIN32
+double drand48()
+{
+	return (double)rand() / RAND_MAX;
+}
+#endif