85be21057a058a0bdb12caac2bae553376442f5a
angie
  Mon Apr 15 10:56:28 2013 -0700
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters.  Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152

diff --git src/inc/annoAssembly.h src/inc/annoAssembly.h
new file mode 100644
index 0000000..dde5d02
--- /dev/null
+++ src/inc/annoAssembly.h
@@ -0,0 +1,24 @@
+/* annoAssembly -- basic metadata about an assembly for the annoGrator framework. */
+
+#ifndef ANNOASSEMBLY_H
+#define ANNOASSEMBLY_H
+
+#include "common.h"
+
+struct annoAssembly
+/* Basic information about a genome assembly. */
+    {
+    char *name;			// UCSC symbolic name for assembly, e.g. "hg19"
+    struct twoBitFile *tbf;	// Opened twoBit sequence file for assembly
+    };
+
+struct annoAssembly *annoAssemblyNew(char *name, char *twoBitPath);
+/* Return an annoAssembly with open twoBitFile. */
+
+uint annoAssemblySeqSize(struct annoAssembly *aa, char *seqName);
+/* Return the number of bases in seq which must be in aa's twoBitFile. */
+
+void annoAssemblyClose(struct annoAssembly **pAa);
+/* Close aa's twoBitFile and free mem. */
+
+#endif//ndef ANNOASSEMBLY_H