From: Heng Li <lh3@live.co.uk>
Date: Sat, 24 Oct 2009 04:41:50 +0000 (+0000)
Subject:  * BUGGY VERSION. Please NOT use it.
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=ed9cedc66455cf33331261e0d230c508411b3df6;p=samtools.git

 * BUGGY VERSION. Please NOT use it.
 * Fixed a minor bug, but the major bug is still there.
---

diff --git a/bam_import.c b/bam_import.c
index 427140d..2b4fb7e 100644
--- a/bam_import.c
+++ b/bam_import.c
@@ -180,27 +180,19 @@ int sam_header_parse_rg(bam_header_t *h)
 
 int sam_header_parse(bam_header_t *h)
 {
-	void *tbl;
 	char **tmp;
 	int i;
 	free(h->target_len); free(h->target_name);
 	h->n_targets = 0; h->target_len = 0; h->target_name = 0;
 	if (h->l_text < 3) return 0;
 	if (h->dict == 0) h->dict = sam_header_parse2(h->text);
-	tbl = sam_header2tbl(h->dict, "SQ", "SN", "LN");
-	h->n_targets = sam_tbl_size(tbl);
-	if (h->n_targets == 0) {
-		sam_tbl_destroy(tbl);
-		return 0;
-	}
+	h->target_name = sam_header2list(h->dict, "SQ", "SN", &h->n_targets);
+	if (h->n_targets == 0) return 0;
+	tmp = sam_header2list(h->dict, "SQ", "LN", &h->n_targets);
 	h->target_len = (uint32_t*)calloc(h->n_targets, 4);
-	h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
-	tmp = (char**)calloc(h->n_targets, sizeof(void*));
-	sam_tbl_pair(tbl, h->target_name, tmp);
 	for (i = 0; i < h->n_targets; ++i)
 		h->target_len[i] = atoi(tmp[i]);
 	free(tmp);
-	sam_tbl_destroy(tbl);
 	return h->n_targets;
 }
 
diff --git a/sam_header.c b/sam_header.c
index fa80050..718bd1d 100644
--- a/sam_header.c
+++ b/sam_header.c
@@ -578,6 +578,43 @@ void *sam_header2tbl(const void *_dict, char type[2], char key_tag[2], char valu
     return tbl;
 }
 
+char **sam_header2list(const void *_dict, char type[2], char key_tag[2], int *_n)
+{
+	const HeaderDict *dict = (const HeaderDict*)_dict;
+    const list_t *l   = dict;
+    int max, n;
+	char **ret;
+
+	ret = 0; *_n = max = n = 0;
+    while (l)
+    {
+        HeaderLine *hline = l->data;
+        if ( hline->type[0]!=type[0] || hline->type[1]!=type[1] ) 
+        {
+            l = l->next;
+            continue;
+        }
+        
+        HeaderTag *key;
+        key   = header_line_has_tag(hline,key_tag);
+        if ( !key )
+        {
+            l = l->next;
+            continue;
+        }
+
+		if (n == max) {
+			max = max? max<<1 : 4;
+			ret = realloc(ret, max * sizeof(void*));
+		}
+		ret[n++] = key->value;
+
+        l = l->next;
+    }
+	*_n = n;
+    return ret;
+}
+
 const char *sam_tbl_get(void *h, const char *key)
 {
 	khash_t(str) *tbl = (khash_t(str)*)h;
@@ -592,21 +629,6 @@ int sam_tbl_size(void *h)
 	return h? kh_size(tbl) : 0;
 }
 
-int sam_tbl_pair(void *h, char **keys, char **vals)
-{
-	khash_t(str) *tbl = (khash_t(str)*)h;
-	int i = 0;
-	khint_t k;
-	if (h == 0) return -1;
-	for (k = kh_begin(tbl); k != kh_end(tbl); ++k) {
-		if (kh_exist(tbl, k)) {
-			keys[i] = (char*)kh_key(tbl, k);
-			vals[i++] = (char*)kh_val(tbl, k);
-		}
-	}
-	return kh_size(tbl);
-}
-
 void sam_tbl_destroy(void *h)
 {
 	khash_t(str) *tbl = (khash_t(str)*)h;
diff --git a/sam_header.h b/sam_header.h
index 5045616..e5c754f 100644
--- a/sam_header.h
+++ b/sam_header.h
@@ -10,10 +10,11 @@ extern "C" {
 	void sam_header_free(void *header);
 	char *sam_header_write(const void *headerDict);   // returns a newly allocated string
 
+	char **sam_header2list(const void *_dict, char type[2], char key_tag[2], int *_n);
+
 	void *sam_header2tbl(const void *dict, char type[2], char key_tag[2], char value_tag[2]);
 	const char *sam_tbl_get(void *h, const char *key);
 	int sam_tbl_size(void *h);
-	int sam_tbl_pair(void *h, char **keys, char **vals);
 	void sam_tbl_destroy(void *h);
 
 #ifdef __cplusplus