13b584581e6d7b1860e0cab97adc3594b1899308
braney
  Mon Aug 7 12:05:10 2023 -0700
add instaPort to bigBed support

diff --git src/hg/inc/liftOver.h src/hg/inc/liftOver.h
index 82c80ce..d27f571 100644
--- src/hg/inc/liftOver.h
+++ src/hg/inc/liftOver.h
@@ -1,23 +1,25 @@
 /* lift genome annotations between assemblies using chain files */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #ifndef LIFTOVER_H
 #define LIFTOVER_H
 
+#include "chain.h"
+
 #define LIFTOVER_MINMATCH        0.95
 #define LIFTOVER_MINBLOCKS       1.00
 
 enum liftOverFileType
 {
     none = 0,
     bed = 1,
     positions = 2,
 };
 
 struct liftOverChain *liftOverChainList();
 /* Get list of all liftOver chains in the central database */
 
 void filterOutMissingChains(struct liftOverChain **pChainList);
 /* Filter out chains that don't exist.  Helps partially mirrored sites. */
@@ -105,19 +107,29 @@
                         double minMatch, double minBlocks, bool fudgeThick,
                       FILE *mapped, FILE *unmapped, boolean multiple);
 /* Lift over file in genePred format. */
 
 void liftOverSample(char *fileName, struct hash *chainHash, 
                         double minMatch, double minBlocks, bool fudgeThick,
                         FILE *mapped, FILE *unmapped);
 /* Open up sample file,  and lift it */
 
 void readLiftOverMap(char *fileName, struct hash *chainHash);
 /* Read map file into hashes. */
 
 char *liftOverErrHelp();
 /* Help message explaining liftOver failures */
 
+char *remapBlockedBed(struct hash *chainHash, struct bed *bed,  
+                             double minMatch, double minBlocks, bool fudgeThick,
+                             bool multiple, char *db, char *chainTable);
+/* Remap blocks in bed, and also chromStart/chromEnd.  If multiple, then bed->next may be
+ * changed to point to additional newly allocated mapped beds, and bed's pointer members may
+ * be free'd so be sure to pass in a properly allocated bed.
+ * Return NULL on success, an error string on failure. */
+
+void liftOverAddChainHash(struct hash *chainHash, struct chain *chain);
+/* Add this chain to the hash of chains used by remapBlockedBed */
 
 #endif