while (*to && *to=='\t') to++;
if ( to-from != 1 ) {
debug("[sam_header_line_parse] multiple tabs on line [%s] (%d)\n", headerLine,(int)(to-from));
+ free(hline);
return 0;
}
from = to;
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;
}
return ret;
}
+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)
+{
+ list_t *l = iter;
+ if ( !l ) return NULL;
+
+ while (l)
+ {
+ HeaderLine *hline = l->data;
+ if ( hline->type[0]!=type[0] || hline->type[1]!=type[1] )
+ {
+ l = l->next;
+ continue;
+ }
+
+ HeaderTag *key, *value;
+ key = header_line_has_tag(hline,key_tag);
+ value = header_line_has_tag(hline,value_tag);
+ if ( !key && !value )
+ {
+ l = l->next;
+ continue;
+ }
+
+ *_key = key->value;
+ *_value = value->value;
+ return l->next;
+ }
+ return l;
+}
+
const char *sam_tbl_get(void *h, const char *key)
{
khash_t(str) *tbl = (khash_t(str)*)h;
return out_dict;
}
+char **sam_header2tbl_n(const void *dict, const char type[2], const char *tags[], int *n)
+{
+ int nout = 0;
+ char **out = NULL;
+
+ *n = 0;
+ list_t *l = (list_t *)dict;
+ if ( !l ) return NULL;
+
+ int i, ntags = 0;
+ while ( tags[ntags] ) ntags++;
+
+ while (l)
+ {
+ HeaderLine *hline = l->data;
+ if ( hline->type[0]!=type[0] || hline->type[1]!=type[1] )
+ {
+ l = l->next;
+ continue;
+ }
+ out = (char**) realloc(out, sizeof(char*)*(nout+1)*ntags);
+ for (i=0; i<ntags; i++)
+ {
+ HeaderTag *key = header_line_has_tag(hline, tags[i]);
+ if ( !key )
+ {
+ out[nout*ntags+i] = NULL;
+ continue;
+ }
+ out[nout*ntags+i] = key->value;
+ }
+ nout++;
+ l = l->next;
+ }
+ *n = nout;
+ return out;
+}