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fixed to handle new exception on matching names/flags/desc
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@ -36,7 +36,7 @@ void parseOptions(int argc, char** argv)
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//
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//
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SwitchArg btest("B","sB", "exist Test B", false);
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SwitchArg btest("B","sB", "exist Test B", false);
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SwitchArg atest("A","sA", "exist Test B", false);
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SwitchArg atest("A","sA", "exist Test A", false);
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ValueArg<string> stest("s", "Bs", "string test", true, "homer",
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ValueArg<string> stest("s", "Bs", "string test", true, "homer",
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"string");
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"string");
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@ -48,11 +48,11 @@ int main(int argc, char** argv)
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"Scoring Matrix name", false,"BLOSUM50","name string");
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"Scoring Matrix name", false,"BLOSUM50","name string");
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cmd.add( scoringMatrixName );
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cmd.add( scoringMatrixName );
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ValueArg<string> seq1Filename ("f","filename1",
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ValueArg<string> seq1Filename ("x","filename1",
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"Sequence 1 filename (FASTA format)", false,"","filename");
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"Sequence 1 filename (FASTA format)", false,"","filename");
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cmd.add( seq1Filename );
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cmd.add( seq1Filename );
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ValueArg<string> seq2Filename ("F","filename2",
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ValueArg<string> seq2Filename ("z","filename2",
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"Sequence 2 filename (FASTA format)", false,"","filename");
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"Sequence 2 filename (FASTA format)", false,"","filename");
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cmd.add( seq2Filename );
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cmd.add( seq2Filename );
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@ -2,8 +2,8 @@ PARSE ERROR: Argument: -n (--name)
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Couldn't find 'mike' in allowed list.
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Couldn't find 'mike' in allowed list.
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Brief USAGE:
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Brief USAGE:
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../examples/test7 [-l <int>] [-u <float lte 1>] [-b <float lte 1>] [-F
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../examples/test7 [-l <int>] [-u <float lte 1>] [-b <float lte 1>] [-z
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<filename>] [-f <filename>] [-s <name string>] [-d]
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<filename>] [-x <filename>] [-s <name string>] [-d]
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[-g <negative int>] [-f <negative int>] -n <homer
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[-g <negative int>] [-f <negative int>] -n <homer
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|marge|bart|lisa|maggie> ... [--] [-v] [-h] <1|2|3>
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|marge|bart|lisa|maggie> ... [--] [-v] [-h] <1|2|3>
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...
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...
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@ -2,8 +2,8 @@ PARSE ERROR: Argument: (--times)
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Couldn't find '6' in allowed list.
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Couldn't find '6' in allowed list.
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Brief USAGE:
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Brief USAGE:
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../examples/test7 [-l <int>] [-u <float lte 1>] [-b <float lte 1>] [-F
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../examples/test7 [-l <int>] [-u <float lte 1>] [-b <float lte 1>] [-z
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<filename>] [-f <filename>] [-s <name string>] [-d]
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<filename>] [-x <filename>] [-s <name string>] [-d]
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[-g <negative int>] [-f <negative int>] -n <homer
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[-g <negative int>] [-f <negative int>] -n <homer
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|marge|bart|lisa|maggie> ... [--] [-v] [-h] <1|2|3>
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|marge|bart|lisa|maggie> ... [--] [-v] [-h] <1|2|3>
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...
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...
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@ -7,7 +7,7 @@ USAGE:
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Where:
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Where:
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-A, --sA
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-A, --sA
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exist Test B
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exist Test A
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-B, --sB
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-B, --sB
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exist Test B
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exist Test B
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@ -1,8 +1,8 @@
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USAGE:
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USAGE:
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../examples/test7 [-l <int>] [-u <float lte 1>] [-b <float lte 1>] [-F
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../examples/test7 [-l <int>] [-u <float lte 1>] [-b <float lte 1>] [-z
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<filename>] [-f <filename>] [-s <name string>] [-d]
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<filename>] [-x <filename>] [-s <name string>] [-d]
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[-g <negative int>] [-f <negative int>] -n <homer
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[-g <negative int>] [-f <negative int>] -n <homer
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|marge|bart|lisa|maggie> ... [--] [-v] [-h] <1|2|3>
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|marge|bart|lisa|maggie> ... [--] [-v] [-h] <1|2|3>
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...
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...
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@ -19,10 +19,10 @@ Where:
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-b <float lte 1>, --lowerBound <float lte 1>
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-b <float lte 1>, --lowerBound <float lte 1>
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(value required) lower percentage bound
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(value required) lower percentage bound
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-F <filename>, --filename2 <filename>
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-z <filename>, --filename2 <filename>
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(value required) Sequence 2 filename (FASTA format)
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(value required) Sequence 2 filename (FASTA format)
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-f <filename>, --filename1 <filename>
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-x <filename>, --filename1 <filename>
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(value required) Sequence 1 filename (FASTA format)
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(value required) Sequence 1 filename (FASTA format)
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-s <name string>, --scoringMatrix <name string>
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-s <name string>, --scoringMatrix <name string>
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