e875e085d0c976ca62b895bdfa5180a942a1854a aamp Thu May 2 14:01:47 2013 -0700 Rolled back some changes to liftOver's presence in the library. If it goes into the top-level maybe it should get some design changes as well. At the moment the design is a bit stretched. diff --git src/hg/inc/liftOver.h src/hg/inc/liftOver.h index 2cd20f7..f501281 100644 --- src/hg/inc/liftOver.h +++ src/hg/inc/liftOver.h @@ -1,121 +1,120 @@ /* lift genome annotations between assemblies using chain files */ #ifndef LIFTOVER_H #define LIFTOVER_H -#ifndef LIFTOVERCORE_H -#include "liftOverCore.h" -#endif +#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 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, 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, 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