X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam_header.h;h=4b0cb03b154efe6e7e14b3dc27182248bb26b427;hb=698a60f0225ea0d46364522db77a559d64b3052a;hp=4f633ed7625c9591cd664387a882e88b0622b490;hpb=d410ecbf60b5aed90ee20c6ba40637ca50241edd;p=samtools.git

diff --git a/sam_header.h b/sam_header.h
index 4f633ed..4b0cb03 100644
--- a/sam_header.h
+++ b/sam_header.h
@@ -1,48 +1,48 @@
 #ifndef __SAM_HEADER_H__
 #define __SAM_HEADER_H__
 
-#include "khash.h"
-KHASH_MAP_INIT_STR(str,const char *)
-
-// HeaderDict is a list_t of header lines. Each HeaderLine holds a list of tags.
-struct _list_t
-{
-    struct _list_t *next;
-    void *data;
-};
-typedef struct _list_t list_t;
-typedef list_t HeaderDict;
-
-typedef struct
-{
-    char key[2];
-    char *value;
-}
-HeaderTag;
+#ifdef __cplusplus
+extern "C" {
+#endif
 
-typedef struct
-{
-    char type[2];
-    list_t *tags;
+	void *sam_header_parse2(const char *headerText);
+	void *sam_header_merge(int n, const void **dicts);
+	void sam_header_free(void *header);
+	char *sam_header_write(const void *headerDict);   // returns a newly allocated string
+
+    /*
+        // Usage example 
+        const char *key, *val; 
+        void *iter = sam_header_parse2(bam->header->text);
+        while ( iter = sam_header_key_val(iter, "RG","ID","SM" &key,&val) ) printf("%s\t%s\n", key,val);
+    */
+    void *sam_header2key_val(void *iter, const char type[2], const char key_tag[2], const char value_tag[2], const char **key, const char **value);
+	char **sam_header2list(const void *_dict, char type[2], char key_tag[2], int *_n);
+
+    /*
+        // Usage example
+        int i, j, n;
+        const char *tags[] = {"SN","LN","UR","M5",NULL}; 
+        void *dict = sam_header_parse2(bam->header->text);
+        char **tbl = sam_header2tbl_n(h->dict, "SQ", tags, &n);
+        for (i=0; i<n; i++)
+        {
+            for (j=0; j<4; j++) 
+                if ( tbl[4*i+j] ) printf("\t%s", tbl[4*i+j]); 
+                else printf("-");
+            printf("\n");
+        }
+        if (tbl) free(tbl);
+     */
+    char **sam_header2tbl_n(const void *dict, const char type[2], const char *tags[], 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);
+	void sam_tbl_destroy(void *h);
+
+#ifdef __cplusplus
 }
-HeaderLine;
-
-
-void debug(const char *format, ...);
-void error(const char *format, ...);
-
-HeaderDict *sam_header_parse(const char *headerText);
-void sam_header_free(HeaderDict *header);
-char *sam_header_write(const HeaderDict *headerDict);   // returns a newly allocated string
-
-khash_t(str) *sam_header_lookup_table(const HeaderDict *dict, char type[2], char key_tag[2], char value_tag[2]);
-
-list_t *list_append(list_t *root, void *data);
-void list_free(list_t *root);
-
-//HeaderDict *sam_header_merge(int n, const HeaderDict **dicts);  // if n=1, the func clones the dictionary
-//char *sam_header_get(const HeaderDict *d, char type[2], int i, char tag[2]);  
-//int sam_header_ins(HeaderDict *d, char tp[2], int i, char tg[2], const char *s);  
-//int sam_header_del(HeaderDict *d, char type[2], int i, char tag[2]);  
+#endif
 
 #endif