be4311c07e14feb728abc6425ee606ffaa611a58 markd Fri Jan 22 06:46:58 2021 -0800 merge with master diff --git src/hg/liftOver/liftOver.c src/hg/liftOver/liftOver.c index 6f2a3a5..c49813b 100644 --- src/hg/liftOver/liftOver.c +++ src/hg/liftOver/liftOver.c @@ -176,32 +176,32 @@ 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); +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")) {