Updated samtools to 0.1.19

[rsem.git] / sam / sam_header.h

diff --git a/sam/sam_header.h b/sam/sam_header.h
index e5c754f3649ce6a13e6f5cb3ca93275d13bb67fe..4b0cb03b154efe6e7e14b3dc27182248bb26b427 100644 (file)
--- a/sam/sam_header.h
+++ b/sam/sam_header.h
@@ -10,8 +10,32 @@ extern "C" {
        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);