diff --git a/src/holders.hpp b/src/holders.hpp index d397855ed..0b1bf2a6e 100644 --- a/src/holders.hpp +++ b/src/holders.hpp @@ -174,7 +174,7 @@ void printStats(StatsHolder const & stats, LambdaOptions const & options) << "\033[0m\n\n"; if (rem != stats.hitsFinal) - std::cout << "WARNING: hits dont add up\n"; + std::cout << "WARNING: hits don't add up\n"; } if (options.verbosity >= 1) diff --git a/src/options.hpp b/src/options.hpp index 7441cf99f..37c8a4f6e 100644 --- a/src/options.hpp +++ b/src/options.hpp @@ -587,14 +587,14 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv) // "STR")); // setValidValues(parser, "query-alphabet", "dna5 aminoacid"); // setDefaultValue(parser, "query-alphabet", "dna5"); -// +// // addOption(parser, ArgParseOption("da", "db-alphabet", // "original alphabet of the subject sequences", // ArgParseArgument::STRING, // "STR")); // setValidValues(parser, "db-alphabet", "dna5 aminoacid"); // setDefaultValue(parser, "db-alphabet", "aminoacid"); -// +// // addOption(parser, ArgParseOption("sa", "seeding-alphabet", // "alphabet to use during seeding (reduction possible)", // ArgParseArgument::STRING, @@ -710,7 +710,7 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv) addSection(parser, "Scoring"); addOption(parser, ArgParseOption("sc", "scoring-scheme", - "'45' for Blosum45; '62' for Blosum62 (default); '80' for Blosum80; " + "use '45' for Blosum45; '62' for Blosum62 (default); '80' for Blosum80; " "[ignored for BlastN]", ArgParseArgument::INTEGER)); setDefaultValue(parser, "scoring-scheme", "62"); @@ -1033,12 +1033,14 @@ parseCommandLine(LambdaIndexerOptions & options, int argc, char const ** argv) // Setup ArgumentParser. ArgumentParser parser("lambda_indexer"); + setShortDescription(parser, "indexer for creating lambda-compatible databases"); + // Define usage line and long description. addUsageLine(parser, "[\\fIOPTIONS\\fP] \\-d DATABASE.fasta\\fP"); sharedSetup(parser); - addDescription(parser, "This is the indexer_binary for creating a lambda-compatible databases."); + addDescription(parser, "This is the indexer_binary for creating lambda-compatible databases."); addSection(parser, "Input Options"); addOption(parser, ArgParseOption("d", "database",