From 2a308f7b0aeed1d06774cacafeaa3a13ca98525a Mon Sep 17 00:00:00 2001
From: Aaron Quinlan <aaronquinlan@gmail.com>
Date: Tue, 21 Apr 2009 10:33:38 -0400
Subject: [PATCH] Changed usage statements to include infor on stdin
1. Changed intersectMain.cpp, complementMain.cpp and mergeMain.cpp to
include information on how to run using stdin.
---
src/intersectBed/intersectMain.cpp | 5 +++++
src/mergeBed/mergeMain.cpp | 5 +++++
2 files changed, 10 insertions(+)
diff --git a/src/intersectBed/intersectMain.cpp b/src/intersectBed/intersectMain.cpp
index 894d0273..0e1d3a6b 100755
--- a/src/intersectBed/intersectMain.cpp
+++ b/src/intersectBed/intersectMain.cpp
@@ -136,6 +136,11 @@ void ShowHelp(void) {
cerr << "\t" << "-f (e.g. 0.05)\t\t" << "Minimum overlap req'd as fraction of a.bed." << endl << "\t\t\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl;
cerr << "\t" << "-c \t\t\t" << "For each entry in A, report the number of hits in B while restricting to -f." << endl << "\t\t\t\tReports 0 for A entries that have no overlap with B." << endl << endl;
cerr << "\t" << "-wb \t\t\t" << "Write the entry in B for each overlap." << endl << "\t\t\t\tUseful for knowing _what_ A overlaps. Restricted by -f." << endl << endl;
+
+ cerr << "NOTES: " << endl;
+ cerr << "\t" << "-i stdin\t\t" << "Allows intersectBed to read BED from stdin. E.g.: cat a.bed | intersectBed -a stdin -b B.bed" << endl << endl;
+
+
// end the program here
exit(1);
diff --git a/src/mergeBed/mergeMain.cpp b/src/mergeBed/mergeMain.cpp
index 08e71223..795ebacb 100755
--- a/src/mergeBed/mergeMain.cpp
+++ b/src/mergeBed/mergeMain.cpp
@@ -102,6 +102,11 @@ void ShowHelp(void) {
cerr << "OPTIONS: " << endl;
cerr << "\t" << "-n\t\t\t" << "Report the number of BED entries that were merged. (=1 if no merging occured)" << endl << endl;
cerr << "\t" << "-d\t\t\t" << "Maximum distance between features allowed for features to be merged. (Default=0)" << endl << endl;
+
+ cerr << "NOTES: " << endl;
+ cerr << "\t" << "-i stdin\t\t" << "Allows mergeBed to read BED from stdin. E.g.: cat a.bed | mergeBed -i stdin" << endl << endl;
+
+
// end the program here
exit(1);
--
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