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
@@ -1,123 +1,135 @@
 /* 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. */
 
 struct liftOverChain *liftOverChainListFiltered();
 /* Get list of all liftOver chains in the central database
  * filtered to include only those chains whose liftover files exist.
  * This helps partially mirrored sites */
 
 struct liftOverChain *liftOverChainForDb(char *fromDb);
 /* Return list of liftOverChains for this database. */
 
 struct liftOverChain *liftOverChainListForDbFiltered(char *fromDb);
 /* Get list of all liftOver chains in the central database for fromDb,
  * filtered to include only those chains whose liftover files exist. */
 
 char *liftOverChainFile(char *fromDb, char *toDb);
 /* Get filename of liftOver chain */
 
 enum liftOverFileType liftOverSniff(char *fileName);
 /* the file-sniffing bit used to distinguish bed from positions files */
 /* returns enum concerning the file type */
 
 int liftOverBed(char *fileName, struct hash *chainHash, 
                         double minMatch,  double minBlocks, 
                         int minSizeT, int minSizeQ,
                         int minChainT, int minChainQ,
                         bool fudgeThick, FILE *f, FILE *unmapped, 
                         bool multiple, bool noSerial, char *chainTable, int *errCt);
 /* Open up file, decide what type of bed it is, and lift it. 
  * Return the number of records successfully converted */
 
 int liftOverBedPlus(char *fileName, struct hash *chainHash, double minMatch,  
                     double minBlocks, int minSizeT, int minSizeQ, int minChainT,
                     int minChainQ, bool fudgeThick, FILE *f, FILE *unmapped, 
                     bool multiple, bool noSerial, char *chainTable, int bedPlus, bool hasBin,
                     bool tabSep, int *errCt);
 /* Lift bed with N+ (where n=bedPlus param) format.
  * Return the number of records successfully converted */
 
 int liftOverBedPlusEnds(char *fileName, struct hash *chainHash, double minMatch,  
                     double minBlocks, int minSizeT, int minSizeQ, int minChainT,
                     int minChainQ, bool fudgeThick, FILE *f, FILE *unmapped, 
                     bool multiple, bool noSerial, char *chainTable, int bedPlus, bool hasBin,
 			bool tabSep, int ends, int *errCt);
 /* Lift bed N+ file.
  * Return the number of records successfully converted */
 
 int liftOverPositions(char *fileName, struct hash *chainHash, 
                       double minMatch,  double minBlocks, 
                       int minSizeT, int minSizeQ,
                       int minChainT, int minChainQ,
                       bool fudgeThick, FILE *f, FILE *unmapped, 
 		      bool multiple, char *chainTable, int *errCt);
 /* Create bed file from positions (chrom:start-end) and lift.
  * Return the number of records successfully converted */
 
 int liftOverBedOrPositions(char *fileName, struct hash *chainHash, 
                         double minMatch,  double minBlocks, 
                         int minSizeT, int minSizeQ,
                         int minChainT, int minChainQ,
 		        bool fudgeThick, FILE *mapped, FILE *unmapped, 
 		        bool multiple, bool noSerial, char *chainTable, int *errCt);
 /* Sniff the first line of the file, and determine whether it's a */
 /* bed, a positions file, or neither. */
 
 char *liftOverRemapRange(struct hash *chainHash, double minRatio,
 			char *chrom, int s, int e, char strand, double minMatch,
 			 char **retChrom, int *retStart, int *retEnd, char *retStrand);
 /* Remap a range through chain hash.  If all is well return NULL
  * and results in retChrom, retStart, retEnd.  Otherwise
  * return a string describing the problem. */
 
 void liftOverGff(char *fileName, struct hash *chainHash, 
                     double minMatch, double minBlocks, 
                     FILE *mapped, FILE *unmapped);
 /* Lift over GFF file */
 
 void liftOverPsl(char *fileName, struct hash *chainHash, 
                             double minMatch, double minBlocks, bool fudgeThick,
                                 FILE *f, FILE *unmapped);
 /* Open up PSL file, and lift it. */
 
 void liftOverGenePred(char *fileName, struct hash *chainHash, 
                         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