5dd57ba4756985d35f8ca72756d963b77934fcf0 angie Thu Jun 7 16:08:53 2018 -0700 Expand support for -multiple to BED 3 to 12 (instead of 4 to 6). refs #18853 Added a -noSerial option to prevent -multiple from forcing the score field to contain a serial number for BED without blocks. Also fixed a bug with the loop on chains overwriting args thickStart and thickEnd. Todo: genePred. Probably won't bother doing PSL because pslMap should be used for that. Also removed some very old #ifdef'd code. diff --git src/hg/liftOver/liftOver.c src/hg/liftOver/liftOver.c index 8d2c4cd..e48e7d1 100644 --- src/hg/liftOver/liftOver.c +++ src/hg/liftOver/liftOver.c @@ -7,49 +7,51 @@ #include "hash.h" #include "options.h" #include "binRange.h" #include "chain.h" #include "bed.h" #include "genePred.h" #include "sample.h" #include "liftOver.h" int bedPlus = 0; int ends = 0; bool fudgeThick = FALSE; bool errorHelp = FALSE; bool multiple = FALSE; +bool noSerial = FALSE; bool hasBin = FALSE; bool tabSep = FALSE; char *chainTable = NULL; static struct optionSpec optionSpecs[] = { {"bedPlus", OPTION_INT}, {"chainTable", OPTION_STRING}, {"errorHelp", OPTION_BOOLEAN}, {"fudgeThick", OPTION_BOOLEAN}, {"genePred", OPTION_BOOLEAN}, {"gff", OPTION_BOOLEAN}, {"hasBin", OPTION_BOOLEAN}, {"minBlocks", OPTION_FLOAT}, {"minChainQ", OPTION_INT}, {"minChainT", OPTION_INT}, {"minMatch", OPTION_FLOAT}, {"minSizeQ", OPTION_INT}, {"minSizeT", OPTION_INT}, {"multiple", OPTION_BOOLEAN}, + {"noSerial", OPTION_BOOLEAN}, {"positions", OPTION_BOOLEAN}, {"pslT", OPTION_BOOLEAN}, {"sample", OPTION_BOOLEAN}, {"ends", OPTION_INT}, {"tab", OPTION_BOOLEAN}, {"tabSep", OPTION_BOOLEAN}, {NULL, 0} }; void usage() /* Explain usage and exit. */ { errAbort( "liftOver - Move annotations from one assembly to another\n" "usage:\n" @@ -74,122 +76,124 @@ " -genePred - File is in genePred format\n" " -sample - File is in sample format\n" " -bedPlus=N - File is bed N+ format\n" " -positions - File is in browser \"position\" format\n" " -hasBin - File has bin value (used only with -bedPlus)\n" " -tab - Separate by tabs rather than space (used only with -bedPlus)\n" " -pslT - File is in psl format, map target side only\n" " -ends=N - Lift the first and last N bases of each record and combine the\n" " result. This is useful for lifting large regions like BAC end pairs.\n" " -minBlocks=0.N Minimum ratio of alignment blocks or exons that must map\n" " (default %3.2f)\n" " -fudgeThick (bed 12 or 12+ only) If thickStart/thickEnd is not mapped,\n" " use the closest mapped base. Recommended if using \n" " -minBlocks.\n" " -multiple Allow multiple output regions\n" + " -noSerial In -multiple mode, do not put a serial number in the 5th BED column\n" " -minChainT, -minChainQ Minimum chain size in target/query, when mapping\n" " to multiple output regions (default 0, 0)\n" " -minSizeT deprecated synonym for -minChainT (ENCODE compat.)\n" " -minSizeQ Min matching region size in query with -multiple.\n" " -chainTable Used with -multiple, format is db.tablename,\n" " to extend chains from net (preserves dups)\n" " -errorHelp Explain error messages\n", LIFTOVER_MINMATCH, LIFTOVER_MINBLOCKS ); } void liftOver(char *oldFile, char *mapFile, double minMatch, double minBlocks, int minSizeT, int minSizeQ, - int minChainT, int minChainQ, bool multiple, char *chainTable, + int minChainT, int minChainQ, bool multiple, bool noSerial, char *chainTable, char *newFile, char *unmappedFile) /* liftOver - Move annotations from one assembly to another. */ { struct hash *chainHash = newHash(0); /* Old chromosome name keyed, chromMap valued. */ FILE *mapped = mustOpen(newFile, "w"); FILE *unmapped = mustOpen(unmappedFile, "w"); int errCt; if (!fileExists(oldFile)) errAbort("Can't find file: %s\n", oldFile); verbose(1, "Reading liftover chains\n"); readLiftOverMap(mapFile, chainHash); verbose(1, "Mapping coordinates\n"); if (optionExists("gff")) { fprintf(stderr, "WARNING: -gff is not recommended.\nUse 'ldHgGene -out=<file.gp>' and then 'liftOver -genePred <file.gp>'\n"); liftOverGff(oldFile, chainHash, minMatch, minBlocks, mapped, unmapped); } else if (optionExists("genePred")) liftOverGenePred(oldFile, chainHash, minMatch, minBlocks, fudgeThick, mapped, unmapped); else if (optionExists("sample")) liftOverSample(oldFile, chainHash, minMatch, minBlocks, fudgeThick, mapped, unmapped); else if (optionExists("pslT")) liftOverPsl(oldFile, chainHash, minMatch, minBlocks, fudgeThick, mapped, unmapped); else if (optionExists("ends")) liftOverBedPlusEnds(oldFile, chainHash, minMatch, minBlocks, minSizeT, minSizeQ, - minChainT, minChainQ, fudgeThick, mapped, unmapped, multiple, + minChainT, minChainQ, fudgeThick, mapped, unmapped, multiple, noSerial, chainTable, bedPlus, hasBin, tabSep, ends, &errCt); else if (optionExists("bedPlus")) liftOverBedPlus(oldFile, chainHash, minMatch, minBlocks, minSizeT, minSizeQ, - minChainT, minChainQ, fudgeThick, mapped, unmapped, multiple, + minChainT, minChainQ, fudgeThick, mapped, unmapped, multiple, noSerial, chainTable, bedPlus, hasBin, tabSep, &errCt); else if (optionExists("positions")) liftOverPositions(oldFile, chainHash, minMatch, minBlocks, minSizeT, minSizeQ, minChainT, minChainQ, fudgeThick, mapped, unmapped, multiple, chainTable, &errCt); else liftOverBed(oldFile, chainHash, minMatch, minBlocks, minSizeT, minSizeQ, - minChainT, minChainQ, fudgeThick, mapped, unmapped, multiple, + minChainT, minChainQ, fudgeThick, mapped, unmapped, multiple, noSerial, chainTable, &errCt); if (!optionExists("positions")) /* I guess liftOverPositions closes these files. This is a little akward though. */ { carefulClose(&mapped); carefulClose(&unmapped); } } int main(int argc, char *argv[]) /* Process command line. */ { int minSizeT = 0; int minSizeQ = 0; int minChainT = 0; int minChainQ = 0; double minMatch = LIFTOVER_MINMATCH; double minBlocks = LIFTOVER_MINBLOCKS; optionInit(&argc, argv, optionSpecs); minMatch = optionFloat("minMatch", minMatch); minBlocks = optionFloat("minBlocks", minBlocks); fudgeThick = optionExists("fudgeThick"); multiple = optionExists("multiple"); +noSerial = optionExists("noSerial"); if ((!multiple) && (optionExists("minSizeT") || optionExists("minSizeQ") || optionExists("minChainT") || optionExists("minChainQ") || - optionExists("chainTable"))) - errAbort("minSizeT/Q, minChainT/Q and chainTable can only be used with -multiple."); + optionExists("chainTable") || optionExists("noSerial"))) + errAbort("minSizeT/Q, minChainT/Q, noSerial and chainTable can only be used with -multiple."); if (optionExists("minSizeT") && optionExists("minChainT")) errAbort("minSizeT is currently a deprecated synonym for minChainT. Can't set both."); minSizeT = optionInt("minSizeT", minChainT); /* note: we're setting minChainT */ minSizeQ = optionInt("minSizeQ", minSizeQ); minChainT = optionInt("minChainT", minChainT); minChainQ = optionInt("minChainQ", minChainQ); bedPlus = optionInt("bedPlus", bedPlus); ends = optionInt("ends", ends); hasBin = optionExists("hasBin"); tabSep = optionExists("tab") || optionExists("tabSep"); if ((hasBin || tabSep) && !bedPlus) usage(); chainTable = optionVal("chainTable", chainTable); if (optionExists("errorHelp")) errAbort("%s", liftOverErrHelp()); if (argc != 5) usage(); liftOver(argv[1], argv[2], minMatch, minBlocks, minSizeT, minSizeQ, - minChainT, minChainQ, multiple, chainTable, argv[3], argv[4]); + minChainT, minChainQ, multiple, noSerial, chainTable, argv[3], argv[4]); return 0; }