0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd max Fri Sep 20 13:18:01 2024 -0700 Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1. diff --git src/hg/liftOver/liftOver.c src/hg/liftOver/liftOver.c index 58c2b35..e5035fa 100644 --- src/hg/liftOver/liftOver.c +++ src/hg/liftOver/liftOver.c @@ -1,225 +1,225 @@ /* liftOver - Move annotations from one assembly to another. */ /* Copyright (C) 2012 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "linefile.h" #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" " liftOver oldFile map.chain newFile unMapped\n" "oldFile and newFile are in bed format by default, but can be in GFF and\n" "maybe eventually others with the appropriate flags below.\n" "The map.chain file has the old genome as the target and the new genome\n" "as the query.\n\n" "***********************************************************************\n" "WARNING: liftOver was only designed to work between different\n" " assemblies of the same organism. It may not do what you want\n" " if you are lifting between different organisms. If there has\n" " been a rearrangement in one of the species, the size of the\n" " region being mapped may change dramatically after mapping.\n" "***********************************************************************\n\n" "options:\n" " -minMatch=0.N Minimum ratio of bases that must remap. Default %3.2f\n" " -gff File is in gff/gtf format. Note that the gff lines are converted\n" " separately. It would be good to have a separate check after this\n" " that the lines that make up a gene model still make a plausible gene\n" " after liftOver\n" " -genePred - File is in genePred format\n" " -sample - File is in sample format\n" " -bedPlus=N - File is bed N+ format (i.e. first N fields conform to bed 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, 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"); if (multiple) errAbort("ERROR: -multiple is not supported for -gff."); if (chainTable) errAbort("ERROR: -chainTable is not supported for -gff."); liftOverGff(oldFile, chainHash, minMatch, minBlocks, mapped, unmapped); } else if (optionExists("genePred")) { if (chainTable) errAbort("ERROR: -chainTable is not supported for -genePred."); liftOverGenePred(oldFile, chainHash, minMatch, minBlocks, fudgeThick, mapped, unmapped, multiple); } else if (optionExists("sample")) { if (multiple) errAbort("ERROR: -multiple is not supported for -sample."); if (chainTable) errAbort("ERROR: -chainTable is not supported for -sample."); liftOverSample(oldFile, chainHash, minMatch, minBlocks, fudgeThick, mapped, unmapped); } else if (optionExists("pslT")) { verbose(1, "Consider using pslMap instead of liftOver for PSL.\n"); if (multiple) errAbort("ERROR: -multiple is not supported for -pslT."); if (chainTable) errAbort("ERROR: -chainTable is not supported for -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, noSerial, chainTable, bedPlus, hasBin, tabSep, ends, &errCt); else if (optionExists("bedPlus")) liftOverBedPlus(oldFile, chainHash, minMatch, minBlocks, minSizeT, minSizeQ, 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, 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 = optionDouble("minMatch", minMatch); minBlocks = optionDouble("minBlocks", minBlocks); fudgeThick = optionExists("fudgeThick"); multiple = optionExists("multiple"); noSerial = optionExists("noSerial"); if ((!multiple) && (optionExists("minSizeT") || optionExists("minSizeQ") || optionExists("minChainT") || optionExists("minChainQ") || 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); if (optionExists("bedPlus")) { bedPlus = optionInt("bedPlus", bedPlus); if (bedPlus < 3 || bedPlus > 15) errAbort("-bedPlus=%d is out of range -- BED has between 3 and 15 fields.", bedPlus); } ends = optionInt("ends", ends); hasBin = optionExists("hasBin"); tabSep = optionExists("tab") || optionExists("tabSep"); -if (hasBin && !bedPlus) +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, noSerial, chainTable, argv[3], argv[4]); return 0; }