From a9683506212b917d07127ebb7c29f495afec044f Mon Sep 17 00:00:00 2001 From: roryk Date: Sat, 2 Jul 2016 09:51:18 -0400 Subject: [PATCH] Remove -u as short option for --umi. The other flag-only arguments don't have a short option, and the -u option wasn't working. --- src/main.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main.cpp b/src/main.cpp index 9288539d..2128ba67 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -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'}, @@ -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