X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=blobdiff_plain;f=bam_aux.c;h=28b22e3059273da57dd8395fba5e29287dc3228b;hp=d6f18ea281712a7d89007d7d87291cbf13718c1b;hb=307c147168f7154e3755712797078c513e0b242a;hpb=63e4e54189bc9e7f43852edf865f95e713b93dc4

diff --git a/bam_aux.c b/bam_aux.c
index d6f18ea..28b22e3 100644
--- a/bam_aux.c
+++ b/bam_aux.c
@@ -1,7 +1,9 @@
 #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)
 {
@@ -18,21 +20,58 @@ void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *d
 	memcpy(b->data + ori_len + 3, data, len);
 }
 
-uint8_t *bam_aux_get(bam1_t *b, const char tag[2])
+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 type, x = (int)s[0]<<8 | s[1];
+		int x = (int)s[0]<<8 | s[1];
 		s += 2;
 		if (x == y) return s;
-		type = toupper(*s); ++s;
-		if (type == 'C') ++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) putchar(*s++); ++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;
 }
@@ -65,43 +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);
 }
 
-void 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;
-	}
-	*ref_id = kh_value(h, iter);
-	if (i == k) { /* dump the whole sequence */
-		*begin = 0; *end = 1<<29; free(s);
-		return;
-	}
-	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;
-	assert(*begin <= *end);
+
+	*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);
+	return *beg <= *end? 0 : -1;
 }
 
 int32_t bam_aux2i(const uint8_t *s)
@@ -152,3 +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