0e64e5ed246694a275e787f67dca8e41ea62d1b8
aamp
  Mon Apr 4 05:57:10 2011 -0700
Added one function to liftOver library code that accepts either bed or position data
diff --git src/hg/inc/liftOver.h src/hg/inc/liftOver.h
index ab7e12a..b8eec6b 100644
--- src/hg/inc/liftOver.h
+++ src/hg/inc/liftOver.h
@@ -1,92 +1,101 @@
 /* lift genome annotations between assemblies using chain files */
 
 #ifndef LIFTOVER_H
 #define LIFTOVER_H
 
 #define LIFTOVER_MINMATCH        0.95
 #define LIFTOVER_MINBLOCKS       1.00
 
 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 */
 
 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, 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, 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 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, 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);
 /* 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 */
 
 
 #endif