struct _HeaderList
{
+ struct _HeaderList *last; // Hack: Used and maintained only by list_append_to_end. Maintained in the root node only.
struct _HeaderList *next;
void *data;
};
const char *r_sq_tags[] = {"SN","LN",NULL};
const char *u_sq_tags[] = {"SN",NULL};
-const char *o_rg_tags[] = {"LB","DS","PU","PI","CN","DT","PL",NULL};
+const char *o_rg_tags[] = {"CN","DS","DT","FO","KS","LB","PG","PI","PL","PU","SM",NULL};
const char *r_rg_tags[] = {"ID",NULL};
const char *u_rg_tags[] = {"ID",NULL};
va_end(ap);
}
+#if 0
+// Replaced by list_append_to_end
static list_t *list_prepend(list_t *root, void *data)
{
list_t *l = malloc(sizeof(list_t));
l->data = data;
return l;
}
+#endif
+
+// Relies on the root->last being correct. Do not use with the other list_*
+// routines unless they are fixed to modify root->last as well.
+static list_t *list_append_to_end(list_t *root, void *data)
+{
+ list_t *l = malloc(sizeof(list_t));
+ l->last = l;
+ l->next = NULL;
+ l->data = data;
+
+ if ( !root )
+ return l;
+
+ root->last->next = l;
+ root->last = l;
+ return root;
+}
static list_t *list_append(list_t *root, void *data)
{
while (*to && *to!='\t') to++;
if ( to-from != 2 ) {
- debug("[sam_header_line_parse] expected '@XY', got [%s]\n", headerLine);
+ debug("[sam_header_line_parse] expected '@XY', got [%s]\nHint: The header tags must be tab-separated.\n", headerLine);
return 0;
}
tag = tags->data;
if ( !tag_exists(tag->key,required_tags[itype]) && !tag_exists(tag->key,optional_tags[itype]) )
{
- debug("Unknown tag [%c%c] for [%c%c].\n", tag->key[0],tag->key[1], hline->type[0],hline->type[1]);
- return 0;
+ // Lower case tags are user-defined values.
+ if( !(islower(tag->key[0]) || islower(tag->key[1])) )
+ {
+ // Neither is lower case, but tag was not recognized.
+ debug("Unknown tag [%c%c] for [%c%c].\n", tag->key[0],tag->key[1], hline->type[0],hline->type[1]);
+ // return 0; // Even unknown tags are allowed - for forward compatibility with new attributes
+ }
+ // else - allow user defined tag
}
tags = tags->next;
}
const char *text;
char *buf=NULL;
size_t nbuf = 0;
+ int tovalidate = 0;
if ( !headerText )
return 0;
while ( (text=nextline(&buf, &nbuf, text)) )
{
hline = sam_header_line_parse(buf);
- if ( hline && sam_header_line_validate(hline) )
- hlines = list_prepend(hlines, hline);
+ if ( hline && (!tovalidate || sam_header_line_validate(hline)) )
+ // With too many (~250,000) reference sequences the header parsing was too slow with list_append.
+ hlines = list_append_to_end(hlines, hline);
else
{
if (hline) sam_header_line_free(hline);