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fix Lintian documentation/man issues #65

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Merged
h-2 merged 1 commit into from
Aug 21, 2016
Merged

fix Lintian documentation/man issues #65

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2 changes: 1 addition & 1 deletion src/holders.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
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10 changes: 6 additions & 4 deletions src/options.hpp
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Expand Up @@ -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,
Expand Down Expand Up @@ -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");
Expand Down Expand Up @@ -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",
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