bfcfffa0ad0401f5264bb656e569a78a12847e12
aamp
  Tue Feb 28 15:59:13 2012 -0800
changed hgLiftOver to only output message out multiple option not being suppported for the positions format ONLY if the input is positions format and if the multiple option is checked
diff --git src/hg/inc/liftOver.h src/hg/inc/liftOver.h
index b8eec6b..f8b48a6 100644
--- src/hg/inc/liftOver.h
+++ src/hg/inc/liftOver.h
@@ -1,101 +1,112 @@
 /* lift genome annotations between assemblies using chain files */
 
 #ifndef LIFTOVER_H
 #define LIFTOVER_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, 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