From 93d12aded2c577bdfddca1ccab9f6e01b1037c34 Mon Sep 17 00:00:00 2001 From: Bryce Lorenz Kille Date: Fri, 18 Aug 2023 19:45:27 -0500 Subject: [PATCH] Correct warning bounds for hg filter --- src/map/include/parseCmdArgs.hpp | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/map/include/parseCmdArgs.hpp b/src/map/include/parseCmdArgs.hpp index 328dbac..e675bd0 100644 --- a/src/map/include/parseCmdArgs.hpp +++ b/src/map/include/parseCmdArgs.hpp @@ -102,7 +102,7 @@ sequences shorter than segment length will be ignored", ArgvParser::OptionRequir cmd.defineOption("noHgFilter", "Don't use the hypergeometric filtering and instead use the MashMap2 first pass filtering."); cmd.defineOption("hgFilterAniDiff", "Filter out mappings unlikely to be this ANI less than the best mapping [default: 0.0]", ArgvParser::OptionRequiresValue); - cmd.defineOption("hgFilterConf", "Confidence value for the hypergeometric filtering [default: 0.999]", ArgvParser::OptionRequiresValue); + cmd.defineOption("hgFilterConf", "Confidence value for the hypergeometric filtering [default: 99.9%]", ArgvParser::OptionRequiresValue); cmd.defineOption("filterLengthMismatches", "Filter mappings where the ratio of reference/query mapped lengths disagrees with the ANI threshold"); @@ -564,11 +564,11 @@ sequences shorter than segment length will be ignored", ArgvParser::OptionRequir if (cmd.foundOption("hgFilterAniDiff")) { str << cmd.optionValue("hgFilterAniDiff"); str >> parameters.ANIDiff; - parameters.ANIDiff /= 100; if (parameters.ANIDiff < 0 || parameters.ANIDiff > 100) { std::cerr << "ERROR, skch::parseandSave, ANI difference must be between 0 and 100" << std::endl; exit(1); } + parameters.ANIDiff /= 100; } else { parameters.ANIDiff = skch::fixed::ANIDiff; } @@ -577,11 +577,11 @@ sequences shorter than segment length will be ignored", ArgvParser::OptionRequir if (cmd.foundOption("hgFilterConf")) { str << cmd.optionValue("hgFilterConf"); str >> parameters.ANIDiffConf; - parameters.ANIDiffConf /= 100; - if (parameters.ANIDiffConf < 0 || parameters.ANIDiffConf > 1) { - std::cerr << "ERROR, skch::parseandSave, hypergeometric confidence must be between 0 and 1" << std::endl; + if (parameters.ANIDiffConf < 0 || parameters.ANIDiffConf > 100) { + std::cerr << "ERROR, skch::parseandSave, hypergeometric confidence must be between 0 and 100" << std::endl; exit(1); } + parameters.ANIDiffConf /= 100; } else { parameters.ANIDiffConf = skch::fixed::ANIDiffConf; }