8f29deda5ff897fbf1d208907ac7f734afc07ed2 jcasper Tue Oct 1 20:31:17 2024 -0700 Many liftOver functions now have a preserveInput argument, which appends the input position to the name field. This makes it easier to see what got mapped where. The option is made available through a command-line argument to the liftOver utility and a checkbox in the hgLiftOver CGI, refs #28023 diff --git src/hg/liftOver/liftOver.c src/hg/liftOver/liftOver.c index e5035fa..65c7bb7 100644 --- src/hg/liftOver/liftOver.c +++ src/hg/liftOver/liftOver.c @@ -34,30 +34,31 @@ {"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}, + {"preserveInput", 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" @@ -83,121 +84,124 @@ " -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", + " -errorHelp Explain error messages\n" + " -preserveInput Attach positions from the input file to item names, to assist in\n" + " determining what got mapped where (bed4+, gff, genePred, sample only)\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) + char *newFile, char *unmappedFile, bool preserveInput) /* 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); + liftOverGff(oldFile, chainHash, minMatch, minBlocks, mapped, unmapped, preserveInput); } else if (optionExists("genePred")) { if (chainTable) errAbort("ERROR: -chainTable is not supported for -genePred."); liftOverGenePred(oldFile, chainHash, minMatch, minBlocks, fudgeThick, - mapped, unmapped, multiple); + mapped, unmapped, multiple, preserveInput); } 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); + mapped, unmapped, preserveInput); } 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); + chainTable, bedPlus, hasBin, tabSep, ends, &errCt, preserveInput); else if (optionExists("bedPlus")) liftOverBedPlus(oldFile, chainHash, minMatch, minBlocks, minSizeT, minSizeQ, minChainT, minChainQ, fudgeThick, mapped, unmapped, multiple, noSerial, - chainTable, bedPlus, hasBin, tabSep, &errCt); + chainTable, bedPlus, hasBin, tabSep, &errCt, preserveInput); 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); + chainTable, &errCt, preserveInput); 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; +bool preserveInput = FALSE; 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); @@ -205,21 +209,23 @@ 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 || tabSep) && !bedPlus) usage(); chainTable = optionVal("chainTable", chainTable); if (optionExists("errorHelp")) errAbort("%s", liftOverErrHelp()); +if (optionExists("preserveInput")) + preserveInput = TRUE; if (argc != 5) usage(); liftOver(argv[1], argv[2], minMatch, minBlocks, minSizeT, minSizeQ, - minChainT, minChainQ, multiple, noSerial, chainTable, argv[3], argv[4]); + minChainT, minChainQ, multiple, noSerial, chainTable, argv[3], argv[4], preserveInput); return 0; }