7df99795b147931dfea8220ed5ab305d11fde6b4
braney
  Thu Mar 10 15:41:46 2022 -0800
move some chromAlias stuff around so bedToBigBed can use a chromAlias
bigBed as a chromAlias file.

diff --git src/inc/bbiAlias.h src/inc/bbiAlias.h
new file mode 100644
index 0000000..b911180
--- /dev/null
+++ src/inc/bbiAlias.h
@@ -0,0 +1,23 @@
+#ifndef BBIALIAS_H
+#define BBIALIAS_H
+
+struct bptIndex   // A structure that contains the field number and the open index of an external index
+{
+struct bptIndex *next;
+int fieldIx;
+struct bptFile *bpt;
+};
+
+struct slName *bbiAliasFindAliases(struct bbiFile *bbi, struct lm *lm, char *seqName);
+/* Find the aliases for a given seqName using an alias bigBed. */
+
+char *bbiAliasFindNative(struct bbiFile *bbi, struct bptIndex *bptIndex, struct lm *lm,  char *alias);
+/* Find the native seqName for a given alias given an alias bigBed. */
+
+struct bptIndex *bbiAliasOpenExtra(struct bbiFile *bbi);
+/* Open any extra indices that this bigBed has. */
+
+unsigned bbiAliasChromSize(struct bbiFile *bbi, struct bptIndex *bptIndex, struct lm *lm, char *chrom);
+/* Find the size of the given chrom in the given chromAlias bbi file.  */
+
+#endif /* BBIALIAS_H */