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Remove -u as short option for --umi. #114

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Remove -u as short option for --umi. #114

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4 changes: 2 additions & 2 deletions src/main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -327,7 +327,7 @@ void ParseOptionsPseudo(int argc, char **argv, ProgramOptions& opt) {
{"single", no_argument, &single_flag, 1},
//{"strand-specific", no_argument, &strand_flag, 1},
{"pseudobam", no_argument, &pbam_flag, 1},
{"umi", no_argument, &umi_flag, 'u'},
{"umi", no_argument, &umi_flag, '1'},
{"batch", required_argument, 0, 'b'},
// short args
{"threads", required_argument, 0, 't'},
Expand Down Expand Up @@ -999,7 +999,7 @@ void usagePseudo(bool valid_input = true) {
<< " pseudoalignment" << endl
<< "-o, --output-dir=STRING Directory to write output to" << endl << endl
<< "Optional arguments:" << endl
<< "-u --umi First file in pair is a UMI file" << endl
<< " --umi First file in pair is a UMI file" << endl
<< "-b --batch=FILE Process files listed in FILE" << endl
<< " --single Quantify single-end reads" << endl
<< "-l, --fragment-length=DOUBLE Estimated average fragment length" << endl
Expand Down