From f510c0b9ba78ba9e37eed979ef9e7433622c89cf Mon Sep 17 00:00:00 2001
From: Aaron Quinlan <aaronquinlan@gmail.com>
Date: Wed, 22 Apr 2009 19:13:59 -0400
Subject: [PATCH] Updated complemeMentMain usage to include stdin example.
---
src/complementBed/complementMain.cpp | 9 ++++-----
1 file changed, 4 insertions(+), 5 deletions(-)
diff --git a/src/complementBed/complementMain.cpp b/src/complementBed/complementMain.cpp
index f70f6c9b..3097c8ce 100755
--- a/src/complementBed/complementMain.cpp
+++ b/src/complementBed/complementMain.cpp
@@ -90,12 +90,11 @@ void ShowHelp(void) {
cerr << "Description: Returns the base pair complement of a BED file." << endl << endl;
cerr << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
- cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed>" << endl << endl;
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed> -g <genome.txt>" << endl << endl;
- //cerr << "OPTIONS: " << endl;
- //cerr << "\t" << "-n\t\t\t" << "Report the number of BED entries that were merged. (=1 if no merging occured)" << endl;
- //cerr << "\t" << "-d\t\t\t" << "Maximum distance between features that will be merged. (Default is 0)" << endl;
- //cerr << "\t\t\t\t" << "For example, \"-d 50\" will merge features that are <= 50 bp apart." << endl << endl;
+ cerr << "NOTES: " << endl;
+ cerr << "\t" << "-i stdin\t\t" << "Allows complementBed to read BED from stdin. E.g.: cat a.bed | complementBed -i stdin" << endl << endl;
+
// end the program here
exit(1);
--
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